tag:blogger.com,1999:blog-13154456470839023932024-03-10T08:16:04.996+05:30BioGem Blog<i>Ashok Kumar's Blog Site...</i>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.comBlogger77125tag:blogger.com,1999:blog-1315445647083902393.post-662052245544751552024-01-18T21:52:00.000+05:302024-01-18T21:52:58.930+05:30Performing Local BLAST Search using BioEdit<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="http://drive.google.com/uc?export=view&id=1rwABYISB6JJO23rSe22v3XH-i7moPf_6" target="_blank"><img alt="BioEdit BLAST" src="http://drive.google.com/uc?export=view&id=1rwABYISB6JJO23rSe22v3XH-i7moPf_6" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p><a href="http://www.mbio.ncsu.edu/BioEdit/bioedit.html" target="_blank">BioEdit</a> is a free biological sequence alignment editor. It has an intuitive multiple document interface and offers convenient features that make alignment and manipulation of sequences relatively easy on windows desktop computers. Additionally, there are several sequence manipulation and analysis options and links to external analysis programs that facilitate a working environment, allowing users to view and manipulate sequences with simple point-and-click operations.</p>
<p>The <a href="https://thalljiscience.github.io/" target="_blank">BioEdit</a> software provides automated local and web BLAST (<b>B</b>asic <b>L</b>ocal <b>A</b>lignment <b>S</b>earch <b>T</b>ool) searches with a simple graphical user interface (GUI) to the command-line BLAST program. This is a simple video tutorial on how to construct a custom nucleotide/protein database using <a href="https://thalljiscience.github.io/" target="_blank">BioEdit</a> software to support <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi" target="_blank">NCBI BLAST</a>. The tutorial also covers how to perform a query search, specifically pairwise sequence alignment, against the database.</p>
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</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-87083502897663761802023-12-03T17:06:00.005+05:302024-01-17T08:53:48.134+05:30Interactive Phylogenetic Tree Visualization using iTOL<div style="color: black; font-family: "times new roman", serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1hpx37m09FxraP4etA3yF_IGilPmp2SwB" target="_blank"><img alt="iTOL" src="https://drive.google.com/uc?export=view&id=1hpx37m09FxraP4etA3yF_IGilPmp2SwB" style="display: block; margin: 0px auto; padding-bottom: 10px;" /></a>
<p>A <a href="https://www.britannica.com/science/phylogenetics" target="_blank">phylogenetic tree</a> (<i>a.k.a.</i>, cladogram or dendrogram) is a diagrammatic/graphical representation of the genetical/evolutionary relationship of species/organisms/genes. Phylogenetic tree helps to find the common ancestor. The <b>i</b>nteractive <b>T</b>ree <b>O</b>f <b>L</b>ife (<a href="https://itol.embl.de/" target="_blank">iTOL</a>) is an online tool to display and manipulate phylogenetic trees. iTOL offers free access (limited access), standard subscription (unlimited access), and iTOL annotation editor subscription (unlimited and versatile access). It supports user-interactive customizable tree layouts, manual drawing, and annotation. iTOL can visualize trees with 50,000 or more nodes.</p>
<p>This is a simple video tutorial for user interactive visualization of phylogenetic trees using the <a href="https://itol.embl.de/" target="_blank">iTOL</a> tool. The <a href="https://itol.embl.de/" target="_blank">iTOL</a> tool produces phylogenetic trees in various formats, such as rectangular, slanting, curved, radial, and curved. It accepts input in Newick, Nexus, or PhyloXML file format.</p>
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</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-7028697754821793902023-08-22T19:52:00.000+05:302023-08-22T19:52:53.811+05:30Constructing Phylogenetic Tree using MEGA Software<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1zSNrLCcgeKab2N5Ak9461ovHRJytqBgg" target="_blank"><img alt="MEGA 11" src="https://drive.google.com/uc?export=view&id=1zSNrLCcgeKab2N5Ak9461ovHRJytqBgg" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p>A <a href="https://www.britannica.com/science/phylogenetics" target="_blank">phylogenetic tree</a> (<i>a.k.a.</i>, cladogram or dendrogram) is a diagrammatic/graphical representation of the genetical/evolutionary relationship of species/organisms/genes. It helps to find the common ancestor. Construction of a phylogenetic tree consists of two phases, multiple sequence alignment and computing distance matrix.</p>
<p>This is a simple video tutorial for constructing a phylogenetic tree using Molecular Evolutionary Genetics Analysis (<a href="https://www.megasoftware.net/" target="_blank">MEGA</a>) software. The <a href="https://www.megasoftware.net/" target="_blank">MEGA</a> software produces phylogenetic trees from multiple sequences in various formats: rectangular, slanting, curved, radial, and curved.</p>
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</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-65748714031746902572023-05-20T23:12:00.000+05:302023-05-20T23:12:42.963+05:30Network Marketing - a silent boom<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1X45zvpBdf962NrY7YhfRLftRTkwAew9D" target="_blank"><img alt="Network Marketing Firms" src="https://drive.google.com/uc?export=view&id=1X45zvpBdf962NrY7YhfRLftRTkwAew9D" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p>Network marketing (a.k.a. direct selling) is a trending business model which replaces the traditional sales and advertising system. It relies on person-to-person sales (chain system) through work from home. Digital marketing (or online marketing) is a way to expand the marketing network through the internet and digital platforms such as PC/laptops and smartphones using digital media and platforms to promote the products. Social media applications place a significant role in sharing product or service details and communicating with persons.</p>
<p>Many local and global network marketing companies are emerging rapidly. Some of the most popular network marketing firms are Altos, Amway, Asclepius Wellness, Atomy India, Avon, Biosash, Forever, Future Maker, Galway, Happy Health India, Herbalife India, Highrich, IMC, Indusviva, Keva Industries, Mary Kay, MI Lifestyle, Modicare, Naswiz Retails, Netsurf Network, OK Life Care, Oriflame, RCM, Renatus Wellness, Rodan+Fields, Safe Shop India, Tupperware, Vestige, etc. We may have known at least one of them in our lifetimes through friends or relatives.</p>
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<a href="https://www.altosindia.net/" target="_blank">
<img alt="Altos" src="https://drive.google.com/uc?export=view&id=19L51ZVgcCexvlfloJy93Ni2NElmCEAsD" width="300" height="300" />
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<a href="https://www.amway.in/" target="_blank">
<img alt="Amway" src="https://drive.google.com/uc?export=view&id=1ocEOV-MVUCLEc0yqnInsDqAWzKvjLRCo" width="300" height="300" />
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<a href="https://www.asclepiuswellness.com/" target="_blank">
<img alt="Asclepius Wellness" src="https://drive.google.com/uc?export=view&id=1JUhJoiFFDhKgfOLl2vvinbWb0UBVmrlC" width="300" height="300" />
</a>
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<a href="https://www.atomy.com/in" target="_blank">
<img alt="Atomy India" src="https://drive.google.com/uc?export=view&id=1dnd4h9WyKfPW9livV3SgTZWbSQZjMoTG" width="300" height="300" />
</a>
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<a href="https://www.avon.co.in/" target="_blank">
<img alt="Avon" src="https://drive.google.com/uc?export=view&id=1cCb8kDtO9_HimM0BqOGCnv1aJp6wW09h" width="300" height="300" />
</a>
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<a href="https://www.biosashbusiness.com/" target="_blank">
<img alt="Biosash" src="https://drive.google.com/uc?export=view&id=11u3Z1DUPJYTVSDCLOtBLeDnMP0WYXlAX" width="300" height="300" />
</a>
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<a href="https://foreverliving.com/" target="_blank">
<img alt="Forever" src="https://drive.google.com/uc?export=view&id=1I3k5GfG21K62gagTa_xxv--MhMqR4t-X" width="300" height="300" />
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<a href="https://futuremaker.in/" target="_blank">
<img alt="Future Maker" src="https://drive.google.com/uc?export=view&id=1_l7ln9pUNEveqcE7aKBFnAaVh3TEvyef" width="300" height="300" />
</a>
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<a href="https://www.glazegalway.com/" target="_blank">
<img alt="Galway" src="https://drive.google.com/uc?export=view&id=1cs5PcKkIt00VAO-Fpyf3PzN3hF3VR0Vw" width="300" height="300" />
</a>
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<a href="https://happyhealthindia.co.in/" target="_blank">
<img alt="Happy Health India" src="https://drive.google.com/uc?export=view&id=1UkbSbEUcH9bPR-MgNXRyyCFWF8iwxUpv" width="300" height="300" />
</a>
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<a href="https://www.herbalife.co.in/" target="_blank">
<img alt="Herbalife India" src="https://drive.google.com/uc?export=view&id=1HVSRCKEK2i5jTMZp0kEZxUuupulhtlkw" width="300" height="300" />
</a>
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<a href="https://www.highrich.net/" target="_blank">
<img alt="Highrich" src="https://drive.google.com/uc?export=view&id=1x51YOY1ijxvF667bVszIgs-_G0xC2Egh" width="300" height="300" />
</a>
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<a href="https://www.imcbusiness.com/" target="_blank">
<img alt="IMC" src="https://drive.google.com/uc?export=view&id=1Gt6fA0KfOLhvqSLzQIrx5R4YDOgEfu0G" width="300" height="300" />
</a>
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<a href="https://indusviva.com/" target="_blank">
<img alt="Indusviva" src="https://drive.google.com/uc?export=view&id=1gjidsOFL9rBOZj-pXzb7zuEXzSxPBjyo" width="300" height="300" />
</a>
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<a href="https://www.kevaind.org/" target="_blank">
<img alt="Keva Industries" src="https://drive.google.com/uc?export=view&id=1UWyOm1YoekSKtHVwPtivW4V0INi5Pqmd" width="300" height="300" />
</a>
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<a href="https://www.marykay.com/" target="_blank">
<img alt="Mary Kay" src="https://drive.google.com/uc?export=view&id=1PK3lDYGFBmMG_yx59Xf3UwKDsBqexYgB" width="300" height="300" />
</a>
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<a href="https://www.milifestylemarketing.com/" target="_blank">
<img alt="MI Lifestyle" src="https://drive.google.com/uc?export=view&id=1AY5JK_igU8of74lLK7CaUseF-jNovSld" width="300" height="300" />
</a>
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<a href="https://www.modicare.com/" target="_blank">
<img alt="Modicare" src="https://drive.google.com/uc?export=view&id=1i3rPn952H-XgGS0-7ahaTf-XrJflr0PN" width="300" height="300" />
</a>
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<a href="https://myshopwiz.com/" target="_blank">
<img alt="Naswiz Retails" src="https://drive.google.com/uc?export=view&id=1lcXE0PdoJCEy5HBbeV19tPTTpZIDvsVY" width="300" height="300" />
</a>
</div>
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<a href="https://netsurfnetwork.com/" target="_blank">
<img alt="Netsurf Network" src="https://drive.google.com/uc?export=view&id=1U44FkdTwkLOq8AbPh1GBwBzHGUUC_6kV" width="300" height="300" />
</a>
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<a href="https://www.oklifecare.com/" target="_blank">
<img alt="OK Life Care" src="https://drive.google.com/uc?export=view&id=1Zs_S3HylOhRwnHPfLeOmjezYoY_CSuSP" width="300" height="300" />
</a>
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<div class="thumbnail">
<a href="https://in.oriflame.com/" target="_blank">
<img alt="Oriflame" src="https://drive.google.com/uc?export=view&id=1duBebD-3_zedB2Ch2U2XdldX2rcLTncA" width="300" height="300" />
</a>
</div>
<div class="thumbnail">
<a href="https://www.rcmbusiness.com/" target="_blank">
<img alt="RCM" src="https://drive.google.com/uc?export=view&id=1eBMQIuArOKKtn2NzQE5WPBAco1wKEv_h" width="300" height="300" />
</a>
</div>
<div class="thumbnail">
<a href="https://renatuswellness.net/" target="_blank">
<img alt="Renatus Wellness" src="https://drive.google.com/uc?export=view&id=1YBCBH8T-7A6i14CvX7VBDrsY7bbH1QTf" width="300" height="300" />
</a>
</div>
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<a href="https://www.rodanandfields.com/en-us/" target="_blank">
<img alt="Rodan + Fields" src="https://drive.google.com/uc?export=view&id=1BdIfEKPLTO9gTNHyVU3MmLPH28OJsZ4I" width="300" height="300" />
</a>
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<a href="https://www.safeshopindia.com/" target="_blank">
<img alt="Safe Shop India" src="https://drive.google.com/uc?export=view&id=110NeHJ9DK0lYxzE7gJM5SPpdYYqfVpz6" width="300" height="300" />
</a>
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<div class="thumbnail">
<a href="https://www.tupperwareindia.com/" target="_blank">
<img alt="Tupperware" src="https://drive.google.com/uc?export=view&id=1PSRD_IW_zNdtRboqF7osvJ582Cmk4I4k" width="300" height="300" />
</a>
</div>
<div class="thumbnail">
<a href="https://www.myvestige.com/" target="_blank">
<img alt="Vestige" src="https://drive.google.com/uc?export=view&id=1vA2dGIb1ts-25Qka48uU5WoPBVP65MtQ" width="300" height="300" />
</a>
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<p>Network marketing is generally in a pyramid structure (one-to-many) where the product was sold by the person(s) instead of through shops. The individuals can be a consumer or sellers. Moreover, the individuals in the chain will not get a salary for selling the products. The salesperson acts as an intermediator to the company. They earn by receiving commissions or attractive rewards for selling the products or providing services. Due to this system, the price of the products is most expensive compared to similar products available in the shops. Companies' reason for the claim of price rise is due to the high quality of the product.</p>
<p><b>Note: </b>Even though there are some assuring statements from the salesperson or chain of individuals, we have to check the genuineness of the product and the company. Most people lose their money or cannot make any payback even after investing in their schemes. <b><i>There Ain't No Such Thing as Free Lunch. If its FREE, then you're the product.</i></b></p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-26149321776486035892023-05-11T21:35:00.001+05:302023-05-11T21:50:30.129+05:30Generating 3D Structure Offline using JSME and BALLOON<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1Tr_ODe6-GB4Wz0yXEzzVofP0RNDoRDRa" target="_blank"><img alt="JSME and BALLOON" src="https://drive.google.com/uc?export=view&id=1Tr_ODe6-GB4Wz0yXEzzVofP0RNDoRDRa" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p>JME/JSME is a free and open-source molecule editor developed by <a href="https://peter-ertl.com/index.html" target="_blank">Peter Ertl</a> and Bruno Bienfait. <a href="https://jsme-editor.github.io/" target="_blank">JSME</a> (JavaScript Molecule Editor) is the successor of JME (Java Molecule Editor). JME is a Java applet application converted to JavaScript due to security and portability issues in Java. JSME is a popular lightweight molecule editor application developed so far.</p>
<p>Jmol/JSmol is a free and open-source molecule visualization tool developed by <a href="https://www.stolaf.edu/people/hansonr/" target="_blank">Bob Hanson</a>. <a href="https://jsme-editor.github.io/" target="_blank">JSmol</a> (JavaScript Molecule Viewer) is the successor of Jmol (Java Molecule Viewer). Jmol is a JAR (Java ARchive) application converted to JavaScript due to security and portability issues in Java. Jmol is the most popular molecule visualization tool implemented in many bioinformatics or cheminformatics web applications.</p>
<p>JSmol in collaboration with JSME, has implemented a 2D (<abbr title="Simplified Molecular Input Line Entry System">SMILES</abbr> string) to 3D structure conversion method by integrating the API of the <a href="https://cactus.nci.nih.gov/translate/" target="_blank">CACTUS</a> server. The link to an interactive demo of JSME and JSmol is <a href="https://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm" target="_blank">here</a>.</p>
<a href="https://drive.google.com/uc?export=view&id=1KKKKgA4ui8_r0Z4T1cQhgaGFO947yxng" target="_blank"><img alt="JSME with JSmol" src="https://drive.google.com/uc?export=view&id=1KKKKgA4ui8_r0Z4T1cQhgaGFO947yxng" style="display: block; margin: 0 auto;" /></a>
<p>BALLOON is a free command-line program for 3D molecular model generation and conformational analysis developed by <a href="https://users.abo.fi/mivainio/" target="_blank">Mikko Vainio</a>. It runs on any platform/operating system for which a binary executable has provided. BALLOON creates 3D atomic coordinates from molecular connectivity via distance geometry and conformer ensembles using multi-objective genetic algorithm. It uses MMFF94-type non-polarizable charges and polarizable (conformation-dependent) electronegativity equalization charges (SFKEEM and EEM) for performing geometry optimization. This is a simple video tutorial to build a 3D small molecule by drawing its 2D chemical structure using JSME Molecule Editor and the <a href="http://users.abo.fi/mivainio/balloon/download.php" target="_blank">BALLOON</a> tool.</p>
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</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-44561665826716249322023-05-08T13:02:00.003+05:302023-05-08T13:19:35.070+05:30YouTube Icon with Link in the Video Description<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1BMcyjjXmp_o3FVmL0jwtl_1DehMPRF7E" target="_blank"><img alt="YouTube Description" src="https://drive.google.com/uc?export=view&id=1BMcyjjXmp_o3FVmL0jwtl_1DehMPRF7E" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p>This is a simple and valuable tip for YouTube video uploaders to share the internal and external URLs in the video description. While entering the URLs in the video description, we must type the whole URL. For example, <a href="https://www.biob.in" target="_blank">https://www.biob.in</a> (<b>Not</b> <a href="https://www.biob.in" target="_blank">www.biob.in</a> or <a href="https://www.biob.in" target="_blank">biob.in</a>). Moreover, for YouTube channel names/handles, it must be with full URL (including valid handle name prefix by @). For example, <a href="https://youtube.com/@AKBIT" target="_blank">https://youtube.com/@AKBIT</a> (<b>Not</b> <a href="https://youtube.com/@AKBIT" target="_blank">/@AKBIT</a> or <a href="https://youtube.com/@AKBIT" target="_blank">@AKBIT</a>). YouTube automatically parses the URLs and replaces the YouTube URLs with a YouTube icon. Instead, the handle name can be hyperlinked by typing the <i>at the rate of</i> symbol (<b>@</b>) followed by the handle name <code><small style="background-color:#c0c0c0"><a href="https://youtube.com/@AKBIT" target="_blank" style="text-decoration: none; color: black">@AKBIT</a></small></code>. Meanwhile, you have to select the exact handle from the dropdown list box.</p>
<a href="https://drive.google.com/uc?export=view&id=1PCyVvpuPT2ecKh9-7_E3xR1usyn1c_PE" target="_blank"><img alt="YouTube Handle" src="https://drive.google.com/uc?export=view&id=1PCyVvpuPT2ecKh9-7_E3xR1usyn1c_PE" style="display: block; margin: 0 auto;" /></a>
<h4 style="color: green; font-weight: bold">YouTube Video Description</h4>
<p>A sample YouTube video description with URLs are below,</p>
<pre style="overflow-x: auto !important; white-space: pre-wrap !important; white-space: -moz-pre-wrap !important; white-space: -pre-wrap !important; white-space: -o-pre-wrap !important; word-wrap: break-word !important;"><code><small>A simple video tutorial to convert chemical structures in the image to a 3D molecule using online OSRA (Optical Structure Recognition Application) tool. The resource URL to the webserver is below,
CACTUS OSRA: https://cactus.nci.nih.gov/cgi-bin/osra/index.cgi
Source Code: https://sourceforge.net/projects/osra/
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My Blog: https://www.biob.in
Website: http://www.biogem.org
My Vlog: https://www.youtube.com/AshokKumarBioIT
YouTube Handle: https://youtube.com/@AKBIT
My GitHub: https://github.com/AshokHub
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Music: Little Samba - Quincas Moreira https://youtu.be/56Njy1UOG3U
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#BioGem #biogem.org #BioBIN #biob.in #Bioinformatics #AKBIT #OSRA #3DMolecules #Compound #2D_Compound #CACTUS #NCI</small></code></pre>
<p><b>Note:</b> Only URL links without the YouTube icon will display in the shorts video description.</p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-88322311562552894222023-05-03T12:31:00.001+05:302023-05-03T12:33:28.747+05:30Hydrophobicity plot using BioPython on Google Colab Notebook<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1-W0CLOpaai18Uy4vBVXUPQN6fY3nXSpQ" target="_blank"><img alt="Hydrophobicity plot" src="https://drive.google.com/uc?export=view&id=1-W0CLOpaai18Uy4vBVXUPQN6fY3nXSpQ" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p>A hydrophobicity or lipophilicity plot is a 2D graphical display of the hydrophobic regions in the protein. The Kyte-Doolittle scale was widely used for identifying surface-exposed regions and transmembrane regions. The plot has the amino acid sequence of a protein on its <i>x</i>-axis and a degree of hydrophobicity on its <i>y</i>-axis. The graph regions with a positive value are hydrophobic. There are several hydrophobicity scales have been published for various uses. The commonly used hydrophobicity scales are Kyte-Doolittle scale, Engelman scale (GES scale), Eisenberg scale, Hopp-Woods scale, Cornette scale, Rose scale, and Janin scale. For further details, refer my previous article <a href="https://www.biob.in/2014/05/hydrophobicity-plot-using-biopython.html" target="_blank">https://www.biob.in/2014/05/hydrophobicity-plot-using-biopython.html</a></p>
<h3 style="color: blue; font-weight: bold">Program Implementation</h3>
<p>In this tutorial, I have used <a href="https://colab.research.google.com/" target="_blank">Google Colab Notebook</a> for running the Python program. Click <a href="https://colab.research.google.com/github/AshokHub/Hydrophobicity_Plot/blob/main/Hydrophobicity_Plot.ipynb" target="_blank">here</a> for interactive demo.</p>
<h4 style="color: green; font-weight: bold">Python Program</h4>
<pre><code class="python">try:
import google.colab
!pip install biopython
except ImportError:
pass
import os
import sys
from urllib.request import urlretrieve
import matplotlib.pyplot as plt
from Bio import SeqIO
seq = 'Q9UKY0.fasta'
url = ('https://raw.githubusercontent.com/AshokHub/'
'Datasets/main/Q9UKY0.fasta')
if not os.path.exists(seq):
urlretrieve(url, seq)
for record in SeqIO.parse(seq, 'fasta'):
id = record.id
seq = record.seq
n = len(seq)
kd = { 'A': 1.8,'R':-4.5,'N':-3.5,'D':-3.5,'C': 2.5,
'Q':-3.5,'E':-3.5,'G':-0.4,'H':-3.2,'I': 4.5,
'L': 3.8,'K':-3.9,'M': 1.9,'F': 2.8,'P':-1.6,
'S':-0.8,'T':-0.7,'W':-0.9,'Y':-1.3,'V': 4.2 }
x = range(1, n+1)
y = []
for res in seq:
y.append(kd[res])
fig = plt.figure()
ax = fig.add_axes([0, 0, 1, 1])
ax.plot(x, y, 'b', lw = 0.9)
ax.set_xlim(1, n)
ax.set(xlabel = 'Residue Number',
ylabel = 'Hydrophobicity',
title = 'Hydrophobicity plot for ' + id)
ax.grid(color = 'gray', linestyle = '-', linewidth = 0.5)
plt.show()</code></pre>
<h4 style="color: green; font-weight: bold">Query Sequence</h4>
<pre style="line-height: 22px; font-size: 10pt"><code>>sp|Q9UKY0|PRND_HUMAN Prion-like protein doppel OS=Homo sapiens GN=PRND PE=1 SV=2
MRKHLSWWWLATVCMLLFSHLSAVQTRGIKHRIKWNRKALPSTAQITEAQVAENRPGAFI
KQGRKLDIDFGAEGNRYYEANYWQFPDGIHYNGCSEANVTKEAFVTGCINATQAANQGEF
QKPDNKLHQQVLWRLVQELCSLKHCEFWLERGAGLRVTMHQPVLLCLLALIWLTVK</code></pre>
<p>The query sequence (<a href="https://raw.githubusercontent.com/AshokHub/Datasets/main/Q9UKY0.fasta" target="_blank">Q9UKY0.fasta</a>) used in this program was hosted at GitHub repository.</p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-7667679744391480802023-04-19T13:11:00.003+05:302023-04-20T12:30:08.994+05:30TNEB Bill Calculator (New)<img alt="TNEB" src="https://drive.google.com/uc?export=view&id=1SIXEZJNiA3f9Di6-dx8M2mFTYXJE5NPH" style="display: none;" />
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<p align="center"><font size="4px" color="blue"><b>TNEB Bill Calculator - 2023</b></font><br/><small>(<i>Revised on September 09, 2022</i>)</small>
</p>
<center>
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<b>For Domestic Usage Only</b>
<div style="padding: 6px 0px 6px 0px;">Units Consumed:
<input type="number" style="background-color:white; border: 1px solid red; outline: none;" id="inputunits" name="inputunits" min="1" oninput="validity.valid||(value='');" style="width: 90px;" autofocus required />
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<span id="tariff"><table class="tariff" summary="TANGEDCO September 2022 Tariffs" cellspacing="0" cellpadding="3" width="100%">
<tr style="font-weight: bold; background-color: #e2ffe2;"><td rowspan="2">Units<br/>(<i>u</i>)</td><td rowspan="2">Subsidy<br/>(≤ 100 <i>u</i>)</td><td colspan="2">Unit Range</td><td rowspan="2">Unit<br/>Cost</td></tr>
<tr style="font-weight: bold; background-color: #e2ffe2;"><td>From</td><td>To</td></tr>
<! -- Upto 100 Units -->
<tr><td>≤ 100</td><td>₹ 4.50 × <i>u</i></td><td>1</td><td>100</td><td>₹ 0.00</td></tr>
<! -- Upto 200 Units -->
<tr><td rowspan="2">≤ 200</td><td rowspan="2">₹ 450</td><td>1</td><td>100</td><td>₹ 0.00</td></tr>
<tr><td>101</td><td>200</td><td>₹ 2.25</td></tr>
<! -- Upto 400 Units -->
<tr><td rowspan="3">≤ 400</td><td rowspan="3">₹ 450</td><td>1</td><td>100</td><td>₹ 0.00</td></tr>
<tr><td>101</td><td>200</td><td>₹ 2.25</td></tr>
<tr><td>201</td><td>400</td><td>₹ 4.50</td></tr>
<! -- Upto 500 Units -->
<tr><td rowspan="4">≤ 500</td><td rowspan="4">₹ 450</td><td>1</td><td>100</td><td>₹ 0.00</td></tr>
<tr><td>101</td><td>200</td><td>₹ 2.25</td></tr>
<tr><td>201</td><td>400</td><td>₹ 4.50</td></tr>
<tr><td>401</td><td>500</td><td>₹ 6.00</td></tr>
<! -- Upto 600 Units -->
<tr><td rowspan="4">≤ 600</td><td rowspan="4">₹ 450</td><td>1</td><td>100</td><td>₹ 0.00</td></tr>
<tr><td>101</td><td>400</td><td>₹ 4.50</td></tr>
<tr><td>401</td><td>500</td><td>₹ 6.00</td></tr>
<tr><td>501</td><td>600</td><td>₹ 8.00</td></tr>
<! -- Upto 800 Units -->
<tr><td rowspan="5">≤ 800</td><td rowspan="5">₹ 450</td><td>1</td><td>100</td><td>₹ 0.00</td></tr>
<tr><td>101</td><td>400</td><td>₹ 4.50</td></tr>
<tr><td>401</td><td>500</td><td>₹ 6.00</td></tr>
<tr><td>501</td><td>600</td><td>₹ 8.00</td></tr>
<tr><td>601</td><td>800</td><td>₹ 9.00</td></tr>
<! -- Upto 1000 Units -->
<tr><td rowspan="6">≤ 1000</td><td rowspan="6">₹ 450</td><td>1</td><td>100</td><td>₹ 0.00</td></tr>
<tr><td>101</td><td>400</td><td>₹ 4.50</td></tr>
<tr><td>401</td><td>500</td><td>₹ 6.00</td></tr>
<tr><td>501</td><td>600</td><td>₹ 8.00</td></tr>
<tr><td>601</td><td>800</td><td>₹ 9.00</td></tr>
<tr><td>801</td><td>1000</td><td>₹ 10.00</td></tr>
<! -- Above 1000 Units -->
<tr><td rowspan="7">> 1000</td><td rowspan="7">₹ 450</td><td>1</td><td>100</td><td>₹ 0.00</td></tr>
<tr><td>101</td><td>400</td><td>₹ 4.50</td></tr>
<tr><td>401</td><td>500</td><td>₹ 6.00</td></tr>
<tr><td>501</td><td>600</td><td>₹ 8.00</td></tr>
<tr><td>601</td><td>800</td><td>₹ 9.00</td></tr>
<tr><td>801</td><td>1000</td><td>₹ 10.00</td></tr>
<tr><td colspan="2">> 1000</td><td>₹ 11.00</td></tr>
</table><span>
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</table>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com10tag:blogger.com,1999:blog-1315445647083902393.post-74173900638454982482023-04-01T22:16:00.002+05:302023-04-01T22:18:51.058+05:30Converting image to 3D molecule using CACTUS OSRA<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=15qxDEGNQllnJtumtj_gurnHds9oJqOjN" target="_blank"><img alt="CACTUS OSRA" src="https://drive.google.com/uc?export=view&id=15qxDEGNQllnJtumtj_gurnHds9oJqOjN" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p><a href="https://cactus.nci.nih.gov/osra/" target="_blank">OSRA</a> (Optical Structure Recognition Application) is a free and open-source optical graph recognition program. The stand-alone version of OSRA is a command-line. OSRA converts a graphical representation of chemical structures from images, as they appear in journal articles, patent documents, textbooks, trade magazines etc., to <a href="http://en.wikipedia.org/wiki/SMILES" target="_blank">SMILES</a> (Simplified Molecular Input Line Entry Specification) format. In addition, the online OSRA tool converts the SMILES string to a 3D molecule in SDF (Standard Data File) file format. OSRA can recognize over 90 graphical format documents by parsing vectors through ImageMagick software. The standard file formats include BMP, GIF, ICO, JPEG, PNG, TIFF, WMF, PDF, PS, etc. The <a href="https://cactus.nci.nih.gov/cgi-bin/osra/index.cgi" target="_blank">CACTUS OSRA</a> tool parses the graphical input to a SMILES string and converts it to a 3D molecule. The video tutorial below demonstrates the conversion of a document in GIF format image to a 3D structure.</p>
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<iframe class="riframe" frameBorder="0" src="https://www.youtube.com/embed/2cry38kTf2M"></iframe>
</div>
<p><b>Note</b> that any software designed for optical recognition is unlikely to be perfect, and the output produced might, and probably will, contain errors, so curation by a human knowledgeable in chemical structures is highly recommended.</p>
<p>Try this sample image from the US Patent Office website first: <a href="https://cactus.nci.nih.gov/image/patent.gif" target="_blank">patent.gif</a>.</p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-83791179122222576452023-03-14T23:18:00.000+05:302023-03-14T23:18:40.746+05:30Converting image to 3D molecule using VEGA ZZ OSRA<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=14Tu3rZ6R4f-XnovLs7WDNgr2-lp5S9Ul" target="_blank"><img alt="VEGA ZZ OSRA" src="https://drive.google.com/uc?export=view&id=14Tu3rZ6R4f-XnovLs7WDNgr2-lp5S9Ul" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p><a href="https://www.ddl.unimi.it/cms/index.php?Software_projects:VEGA_ZZ" target="_blank">VEGA ZZ</a> is a free (for non-profit academic uses) molecular modelling suite. It consists of many third-party packages, which act as an interface to the VEGA ZZ software.</p>
<p><a href="https://cactus.nci.nih.gov/osra/" target="_blank">OSRA</a> (Optical Structure Recognition Application) is a free and open-source optical graph recognition program. The stand-alone version of OSRA is a command-line. OSRA converts a graphical representation of chemical structures from images to <a href="http://en.wikipedia.org/wiki/SMILES" target="_blank">SMILES</a> (Simplified Molecular Input Line Entry Specification) format. In addition, the online OSRA tool converts the SMILES string to a 3D molecule in SDF (Standard Data File) file format. OSRA can recognize over 90 graphical format documents by parsing vectors through ImageMagick software. The standard file formats include BMP, GIF, ICO, JPEG, PNG, TIFF, WMF, PDF, PS, etc.</p>
<p><a href="https://drive.google.com/uc?export=view&id=1CI6KS8yFvDWIf_qSjAiIU4DvTQ7KhXAG" target="_blank"><img alt="OSRA" src="https://drive.google.com/uc?export=view&id=1CI6KS8yFvDWIf_qSjAiIU4DvTQ7KhXAG" style="display: block; margin: 0 auto;" /></a></p>
<p>VEGA ZZ consists of an OSRA plug-in that acts as an interface to it. Moreover, it supports imaging devices such as cameras and image scanners for acquiring documents through the TWAIN interface. The VEGA ZZ software parses the graphical input to a SMILES string and converts it to a 3D molecule. The video tutorial below demonstrates the conversion of a document in GIF format image to a 3D structure.</p>
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</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-11939822646949119442023-03-08T18:17:00.000+05:302023-03-08T18:17:21.500+05:30Saving AutoDock Vina Docking Result to PDB using Chimera<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1MywdT9IQuu1qvfHC-dtoR52--JCiI56W" target="_blank"><img alt="Screenshots" src="https://drive.google.com/uc?export=view&id=1MywdT9IQuu1qvfHC-dtoR52--JCiI56W" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p>AutoDock is a free molecular modeling simulation suite mainly used for molecular docking. It consists of two programs, namely AutoGrid and AutoDock. The three variants of AutoDock are <a href="https://autodock.scripps.edu/" target="_blank">AutoDock 4.2.6</a>, <a href="https://vina.scripps.edu/" target="_blank">AutoDock Vina 1.2.3</a> (a successor of AutoDock), and <a href="https://github.com/ccsb-scripps/AutoDock-GPU" target="_blank">AutoDock GPU</a>.</p>
<p>AutoDock or Vina use PDBQT (Protein Data Bank (PDB), Partial Charge (Q), and Atom Type (T)) molecular structure file format for input and output. But, most molecular analysis and visualization tools accept the PDB file format. The video tutorial for converting AutoDock or Vina results in a complex PDBQT file format to PDB file format is below.</p>
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</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-23931722542213362492023-03-03T17:01:00.006+05:302023-03-04T12:33:17.338+05:30RNA Secondary Structure Prediction using Nussinov Algorithm<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
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<a href="https://drive.google.com/uc?export=view&id=1nVyZ0Q3FQfdGirSksFq41pyen7avjwFH" target="_blank"><img alt="Nussinov Algorithm" src="https://drive.google.com/uc?export=view&id=1nVyZ0Q3FQfdGirSksFq41pyen7avjwFH" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p>The <b>Nussinov</b> algorithm is an RNA secondary structure (folding) prediction method using a dynamic programming approach. <b><i>Ruth Nussinov</i></b> introduced this algorithm in the year 1978. It involves computing a two-dimensional (2D) diagonal matrix with the same sequence at both dimensions. The scores are given based on complementary (<b>1</b>) or non-complementary (<b>0</b>) matches of characters. Matrix solving consists of three stages (<i>i</i>) <i>initialization</i>, (<i>ii</i>) <i>matrix-filling</i>, and (<i>iii</i>) <i>trace-back of arrows</i> for structures.</p>
<p>\(\style{ color: blue; } {\begin{array} \\ \text{RNA sequence, } S=a_1a_2a_3....a_{l-1}a_l \\ \begin{align*} \\ \!\!\!\!\! \text{where,} \\ & a=\text{characters (A, U, C, G)} \\ & l=\text{length of the sequence} \\ \end{align*} \end{array}} \)</p>
<p>In this tutorial, I have taken a sample RNA sequence (<i>S</i>) as <b>GGGAAAUCC</b> for prediction.</p>
<h3 style="color: green; padding-bottom: 10px;">Initialization</h3>
<p>The initialization step is to preset the diagonal cells with zero (<b>0</b>) values to perform matrix filling.</p>
<p>\(\style{ color: blue; } {\begin{align} M_{i, i-1}=0 \text{ where, } i=2 \text{ to } l \\ M_{i,i}\quad =0 \text{ where, } i=1 \text{ to } l \\ \end{align}} \)</p>
<p><a href="https://drive.google.com/uc?export=view&id=1Aw0qYUBq0DZuAELQq3SUGGWfvr7Fq4d2" target="_blank"><img alt="Initialization" src="https://drive.google.com/uc?export=view&id=1Aw0qYUBq0DZuAELQq3SUGGWfvr7Fq4d2" style="display: block; margin: 0 auto;" /></a></p>
<p>PS: Here, the diagonal row (<i>M<sub>i,i-1<sub></i>) in the matrix is considered for initialization purpose only.</p>
<h3 style="color: green; padding-bottom: 10px;">Matrix Filling</h3>
<p>The matrix-filling step should be performed using the formula below. The matrix cells are filled with maximum scores and pointers while solving the formula.</p>
<p>\(\style{ color: blue; } {\begin{array} \\ M_{i, j} = \max \begin{cases} M_{i+1, j} & i \text{ unpaired } (\downarrow) \\ M_{i ,j-1} & j \text{ unpaired } (\leftarrow) \\ M_{i+1, j-1} + s(a_i,a_j) & i, j \text{ paired } (\swarrow) \\ \underset{i \lt k \lt j} \max \lbrace M_{i, k} + M_{k+1, j} \rbrace & \text{bifurcation } (\downarrow,\leftarrow) \end{cases} \\ \begin{align*} \kern-1em \text{where,} \\ & s(a_i, a_j) = 0, \text{ if } a_i \text{ and } a_j \text{ are non-complement} \\ & s(a_i, a_j) = 1, \text{ if } a_i \text{ and } a_j \text{ are complement} \end{align*} \end{array}} \)</p>
<p>The maximum score determines the structure of the RNA sequence. There are four possible chances of structures based on the scores.</p>
<p><a href="https://drive.google.com/uc?export=view&id=19EHCPFJM91jj8osT_7a1Nq_EJtzpboSb" target="_blank"><img alt="RNA Foldings" src="https://drive.google.com/uc?export=view&id=19EHCPFJM91jj8osT_7a1Nq_EJtzpboSb" style="display: block; margin: 0 auto;" /></a></p>
<p>An example,</p>
<p>\(\style{ color: blue; } {\begin{array} \\ M_{4,7}=\max \begin{cases} M_{5,7} \\ M_{4,6} \\ M_{5,6}+s(a_4,a_7) \\ \underset{k \in (5,6)} \max \begin{cases} M_{4,5}+M_{6,7} \\ M_{4,6}+M_{7,7} \end{cases} \\ \end{cases} \end{array}} \)</p>
<p>\(\style{ color: blue; } {\begin{array} \\ M_{4,7} = \max \begin{cases} 1 \\ 0 \\ 0+s(\text{A,U}) \\ \max \begin{cases} 0+1 \\ 0+0 \end{cases} \\ \end{cases} & = \max \begin{cases} 1 \\ 0 \\ 0+1 \\ \max \begin{cases} 1 \\ 0 \end{cases} \\ \end{cases} & = \max \begin{cases} 1 \\ 0 \\ 1 \\ 1 \\ \end{cases} & = 1 \end{array}} \)</p>
<p>\(\style{ color: blue; } {\begin{array} \\ M_{4,7}=\text{pointers} \begin{cases} M_{5,7} \ (\downarrow )\\ M_{4,6} \\ M_{5,6} \ (\swarrow) \\ M_{4,5} \ (\leftarrow), M_{6,7} \ (\downarrow) \\ \end{cases} \end{array}} \)</p>
<p>The completed matrix-filling is below.</p>
<p><a href="https://drive.google.com/uc?export=view&id=1RfI0PtzJGL_9WG08Ak_cgKEq1LnoqXbf" target="_blank"><img alt="Matrix Filling" src="https://drive.google.com/uc?export=view&id=1RfI0PtzJGL_9WG08Ak_cgKEq1LnoqXbf" style="display: block; margin: 0 auto;" /></a></p>
<h3 style="color: green; padding-bottom: 10px;">Trace Back</h3>
<p>The secondary structure of the RNA sequence can be predicted by tracing back the arrows from the right-most cell in the first row towards to half-diagonal in the matrix. <u>There can be many possible structures.</u> The best optimal structure is predicted by tracing arrow having high scores or diagonal arrows (↙) in the cell.</p>
<p>The final completed trace-back matrix with pointers by preferring high scores is below.</p>
<p><a href="https://drive.google.com/uc?export=view&id=1TsmB_PHuBNHZpmocmFVW82mSfsqMO_Iu" target="_blank"><img alt="Trace Back" src="https://drive.google.com/uc?export=view&id=1TsmB_PHuBNHZpmocmFVW82mSfsqMO_Iu" style="display: block; margin: 0 auto;" /></a></p>
<p>The RNA secondary structure by tracing the pointers is below.</p>
<p><a href="https://drive.google.com/uc?export=view&id=1GSp9ZASESPipsJot7V3m4VB0Y4BV5kfe" target="_blank"><img alt="RNA Structure" src="https://drive.google.com/uc?export=view&id=1GSp9ZASESPipsJot7V3m4VB0Y4BV5kfe" style="display: block; margin: 0 auto;" /></a></p>
<p>The secondary structure for the RNA sequence <code><b style="color: blue">GGGAAAUCC</b></code> in bracket-notation model is <code><b style="color: blue">.(((..)))</b></code>.</p>
<h3 style="color: green; padding-bottom: 10px;">Video Tutorial</h3>
<p style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="270" width="480" src="https://www.youtube.com/embed/hwhLBfA3mgY"></iframe>
</p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-55953346538018895082023-01-15T22:22:00.000+05:302023-01-15T22:22:11.181+05:30Taking High Resolution Web-Page Screenshots on Chrome<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1ArRMRE1K76jKQc878mhoDB2oZNRuXs-V" target="_blank"><img alt="Screenshots" src="https://drive.google.com/uc?export=view&id=1ArRMRE1K76jKQc878mhoDB2oZNRuXs-V" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p><a href="https://www.google.com/intl/en_in/chrome/" target="_blank">Google Chrome</a> (or simply Chrome) is a free and fast web browser developed by <a href="https://www.google.com/" target="_blank">Google</a>. The currently released Chrome web browser comes with built-in functionality to take a screenshot of webpages without any add-ons. It allows taking a high-quality screenshots at high resolutions.</p>
<h3 style="color: blue">Types of Screenshots</h3>
<p>The Chrome browser support taking 4 types of screenshots of a web page.</p>
<ul style="list-style-type:circle">
<li><b>Capture area screenshot</b> - taking screenshot on specific region</li>
<li><b>Capture full size screenshot</b> - taking scrolling screenshot from top to bottom</li>
<li><b>Capture node screenshot</b> - taking screenshot of a specific HTML element</li>
<li><b>Capture screenshot</b> - taking full screen screenshot</li>
</ul>
<p>The <i>Capture full size screenshot</i>/<i>Capture screenshot</i> options are accessible via <b>Chrome's developer tools</b> (Ctrl+Shift+I). Furthermore, <i>Capture area screenshot</i>/<i>Capture node screenshot</i> options are accessible via <b>Run command</b> (Ctrl+Shift+P) by entering command “<i>screenshot</i>”.</p>
<p><a href="https://drive.google.com/uc?export=view&id=1AjxzqamiPtteUiQFYgTw_o9RsbiQekre" target="_blank"><img alt="Run command" src="https://drive.google.com/uc?export=view&id=1AjxzqamiPtteUiQFYgTw_o9RsbiQekre" style="display: block; margin: 0 auto;" /></a></p>
<p>The video tutorial below demonstrates various types of webpage image capture methods.</p>
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</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com2tag:blogger.com,1999:blog-1315445647083902393.post-72034205895169824832023-01-04T12:10:00.001+05:302023-01-04T12:16:46.963+05:30Protein-Ligand Binding Site Analysis using Chimera<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1KnPnirA2ada4GUh9zcfv4OPB7SofpGfC" target="_blank"><img alt="Run command" src="https://drive.google.com/uc?export=view&id=1KnPnirA2ada4GUh9zcfv4OPB7SofpGfC" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p>Chimera (or <a href="https://www.cgl.ucsf.edu/chimera/" target="_blank">UCSF Chimera</a>) is an interactive molecular visualization and analysis program developed by the Resource for Biocomputing, Visualization, and Informatics (<a href="http://rbvi.ucsf.edu/" target="_blank">RBVI</a>) at the University of California, San Francisco (<a href="https://www.ucsf.edu/" target="_blank">UCSF</a>). ChimeraX (or <a href="https://www.cgl.ucsf.edu/chimerax/" target="_blank">UCSF ChimeraX</a>) is the next-generation molecular visualization program, which is a successor of Chimera. The Chimera/ChimeraX program supports analyzing various molecular structures and related data, including sequence alignments, docking results, molecular assemblies, electron density maps, trajectories, and conformational ensembles. It can be downloaded freely for academic, government, nonprofit, and personal use.</p>
<h3 style="color: blue; padding-bottom: 10px;">Protein-Ligand Interaction Models</h3>
<p>In the protein-ligand interaction model, proteins or ligands are represented by a wire-frame model / stick model / ball-and-stick model / cartoon model / space-fill model / surface model, but not both. The interactions between protein and ligand atoms is represented by dotted or dashed lines. This is a video tutorial for prediction of protein-ligand atom interactions and Ramachandran plot using Chimera tool. In this tutorial, I have used a Ascaris hemoglobin domain protein structure retrieved from the <a href="https://www.rcsb.org" target="_blank">Protein Data Bank</a> (PDB ID: <a href="https://www.rcsb.org/structure/3C33" target="_blank">3C33</a>).</p>
<p><b>Note:</b> In Chimera, atoms/molecules are selected by three methods: (<i>i</i>) Ctrl+Left-click for one atom section, (<i>ii</i>) Ctrl+Shift+Left-click for two atoms section, and (<i>iii</i>) Ctrl+Left-click+Up Arrow for whole molecule section.</p>
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</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-64773033948087294282022-09-03T13:26:00.069+05:302022-10-16T13:14:28.858+05:30PCA, PCoA, and Tree Plot using NTSYSpc<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1ED6uGG3gV7NvusyPXLRFA0Nc0JjvFlEc" target="_blank"><img alt="PCA Input" src="https://drive.google.com/uc?export=view&id=1ED6uGG3gV7NvusyPXLRFA0Nc0JjvFlEc" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a>
<p>This tutorial explains how to perform <u><b>P</b></u>rincipal <u><b>C</b></u>omponent <u><b>A</b></u>nalysis (PCA) and <u><b>P</b></u>rincipal <u><b>C</b></u>oordinate <u><b>A</b></u>nalysis (PCoA) of multivariate data using the <a href="https://www.exetersoftware.com/cat/ntsyspc/ntsyspc.html" target="_blank">NTSYSpc</a> tool. NTSYSpc (<u><b>N</b></u>umerical <u><b>T</b></u>axonomy and Multivariate Analysis <u><b>SYS</b></u>tem for <u><b>p</b></u>ersonal <u><b>c</b></u>omputer) is a simple and efficient statistical tool used to find patterns and display structures in multivariate data. The tool used in this tutorial is <a href="https://www.appliedbiostat.com/ntsyspc/ntsyspc.html" target="_blank">NTSYSpc v2.11a</a>.</p>
<p>In this tutorial, I have used a sample allelic data matrix (shown below). The matrix file consists of molecular weight size marker (rows) and sample/loci (columns).</p>
<p>\[M_{mw,s}=\begin{bmatrix}0&0&1&1&0&0\\0&0&1&0&0&0\\0&0&1&1&0&0\\0&0&1&1&1&1\\1&1&1&0&0&0\\0&1&1&1&0&0\\0&0&1&1&1&1\\0&0&0&0&1&1\\1&0&0&0&0&0\\1&1&0&0&0&0\\1&1&0&0&0&0\\0&1&0&0&0&0\end{bmatrix}\]</p>
<p>The NTSYSpc tool accepts various format files namely: NTSYSpc dataset (.NTS) file, NTSYSpc batch (.NTB) file, Microsoft Excel Worksheet (.XLS/.XLSX) file, Comma Separated Values (.CSV) file, and MatLab (.M) file for input/export. It will run in interactive mode (step-by-step procedure) or batch mode (command lines). The NTSYSpc data editor (NTedit) preview of the sample data matrix is below.</p>
<p><a href="https://drive.google.com/uc?export=view&id=11EPICoYNEy6gO5bP3tIV-eoH_9t3BnRo" target="_blank"><img alt="Marker Matrix" src="https://drive.google.com/uc?export=view&id=11EPICoYNEy6gO5bP3tIV-eoH_9t3BnRo" style="display: block; margin: 0 auto;" /></a></p>
<p>The common program parameters used in the NTSYSpc batch file are: <i><b>o</b></i>—input data matrix file; <i><b>r</b></i>—output similarity or dissimilarity matrix file; <i><b>output</b></i>—display matrix file; <i><b>c</b></i>—type of coefficient; <i><b>d</b></i>—direction of reading the matrix, <i><b>row</b></i> (checked by default)–reading matrix by rows as the variables and <i><b>col</b></i>–reading matrix by columns as the variables; <i><b>corr</b></i>–Pearson correlation coefficient; <i><b>n</i></b>—sample sizes for each coefficient (or) dimensions of the output matrix (default is 3); <i><b>val</i></b>—eigenvalue matrix file; and <i><b>f</b></i>—feature vector matrix file.</p>
<h3 style="color: red; padding-bottom: 10px;">NTSYSpc File Format</h3>
<p>An NTSYSpc matrix consists of 4 records: comments, matrix parameter line, row and column labels, and matrix data lines.</p>
<p><b>1. Comments (</b>optional<b>)</b> – <i>comment line describing the data</i>. The first character in each line must begin with double quotation mark (") or single quotation mark/apostrophe (') symbol.</p>
<p><b>2. Matrix Parameter Line</b> – <i>type and dimension of the matrix</i>. This line contains 4 integer numbers (the second and third may have a suffix letter to indicate the presence and location of row and column labels) separated by at least one blank space. The <i>first</i> number represents the type of matrix, (<b>1</b>) rectangular data matrix, (<b>2</b>) symmetric dissimilarity matrix, (<b>3</b>) symmetric similarity matrix, (<b>4</b>) diagonal matrix, (<b>5</b>) tree matrix for dissimilarity data, (<b>6</b>) tree matrix for similarity data, (<b>7</b>) graph matrix for dissimilarity data, and (<b>8</b>) graph matrix for similarity data. The <i>second</i> and <i>third</i> number repesents rows and columns of the matrix. It may consist of suffix letters “<b>B</b>”, “<b>E</b>”, or “<b>L</b>” to indicate the presence of labels in the matrix. Whereas, “<b>B</b>” indicates first element at the beginning of each row in the matrix, “<b>E</b>” indicates last element at the end of each row in the matrix, and “<b>L</b>” indicates separate list of row and/or column labels (seperated by new line for row labels and column labels) before starting the matrix lines. The <i>fourth</i> number is <b>0</b> if there are no missing data in the matrix. If there are missing data then the fourth number should be a <b>1</b> followed by at least one blank and then the numerical code used to denote the missing values - <b>999</b> is a popular choice. The code should not be a value that could result from standardization or other transformations of the data matrix (e.g., do not use <b>0</b> if you are going to standardize the data).</p>
<p><b>3. Row and Column Labels</b> – <i>labels of rows and columns</i>. Labels must be furnished if a “<b>B</b>”, “<b>E</b>”, or “<b>L</b>” is placed after the numbers of rows and/or “<b>L</b>” after the number of columns in the matrix parameter line. When the results are plotted the underscore character “<b>_</b>” is displayed as a blank.</p>
<p><b>4. Matrix Data Lines</b> – <i>data matrix in lines</i>. The elements of the matrix are entered row wise corresponding to one or more lines. Whereas, symmetric matrices are entered row wise in left diagonal starting with column 1 and ending with the diagonal elements (i.e., the lower half matrix). If all the elements for a row do not fit on a single line, then you may continue typing on as many new lines as needed. It is important that the first element of a new row starts on a new line—even if the previous line is mostly empty. The elements themselves are free format. Values must be separated by one or more blanks or by a comma.</p>
<p>Example, the input data matrix in NTSYSpc file format is below:</p>
<pre style="font-size: small; color:blue;">"Marker - Molecular weight x Locus
1 12B 6L 0
S_1 S_2 S_3 S_4 S_5 S_6
3000 0 0 1 1 0 0
2500 0 0 1 0 0 0
2400 0 0 1 1 0 0
2000 0 0 1 1 1 1
1600 1 1 1 0 0 0
1500 0 1 1 1 0 0
1000 0 0 1 1 1 1
700 0 0 0 0 1 1
600 1 0 0 0 0 0
500 1 1 0 0 0 0
400 1 1 0 0 0 0
120 0 1 0 0 0 0</pre>
<p>More than one matrix can be stored in a single file. The records for a second matrix (starting with the optional comment lines) directly follow after those for the first.</p>
<h3 style="color: red; padding-bottom: 10px;">Principal Component Analysis</h3>
<p>Principal component analysis (a.k.a. dimensionality reduction method) is a type of ordination analysis method used to reduce high-dimensional data into low-dimensional data without eliminating the preliminary information.</p>
<p>The following batch file will standardize a data matrix to variables by rows, compute correlation matrix (i.e., similarity or dissimilarity indices), extract the first 3 PCA axes from the correlation matrix by computing eigenvectors and eigenvalues, project the standardized data onto these eigenvectors (i.e., feature vector), and then make a 3-dimensional (3D) plot of the projections (objects).</p>
<code style="font-size: small; color:blue;">*stand o=data.nts r=sdata.nts d=row<br/>
*simint o=sdata.nts r=corr.nts c=corr d=row<br/>
*eigen o=corr.nts r=vect.nts val=val.nts n=3<br/>
*proj o=sdata.nts r=proj.nts f=vect.nts d=col<br/>
*mod3d o=proj.nts s=data.nts</code>
<p><a href="https://drive.google.com/uc?export=view&id=1xcc-1w7aWcQpRIBXi5rxkdjMwgy0hFBL" target="_blank"><img alt="NTSYS PCA" src="https://drive.google.com/uc?export=view&id=1xcc-1w7aWcQpRIBXi5rxkdjMwgy0hFBL" style="display: block; margin: 0 auto;" /></a></p>
<h3 style="color: red; padding-bottom: 10px;">Principal Coordinate Analysis</h3>
<p>PCoA is an alternative to PCA which will give the same results as PCA. It converts data on distances between objects into map-based visualization for better understanding objects that are similar or dissimilar. Moreover, it allows you to identify groups or clusters. When there are fewer points than variables, the computation time will be much less than for the PCA.</p>
<p>The following batch file will standardize a data matrix by variables (rows), compute similarity or dissimilarity coefficient for the data matrix, factorize double-centered distance matrix, compute eigenvectors and eigenvalues corresponding to projections (objects), and then make a 3D plot of the projections in column-wise.</p>
<code style="font-size: small; color:blue;">*stand o=data.nts r=sdata.nts d=row<br/>
*simint o=sdata.nts r=dist.nts c=corr<br/>
*dcenter o=dist.nts r=dcent.nts<br/>
*eigen o=dcent.nts r=proj.nts val=val.nts<br/>
*mod3d o=proj.ntss=data.nts d=col</code>
<p><a href="https://drive.google.com/uc?export=view&id=12MC7YnPwwqAN0xnSBKPLchXJXG0OYTd5" target="_blank"><img alt="NTSYS PCoA" src="https://drive.google.com/uc?export=view&id=12MC7YnPwwqAN0xnSBKPLchXJXG0OYTd5" style="display: block; margin: 0 auto;" /></a></p>
<h3 style="color: red; padding-bottom: 10px;">Tree Plot</h3>
<p>The phenogram (numerical taxonomy—classification based on characters) of the allelic data matrix have constructed by computing the similarity or dissimilarity matrix. Furthermore, the similarity or dissimilarity matrix have reconstructed to UPGMA (<u>U</u>nweighted <u>P</u>air <u>G</u>roup <u>M</u>ethod with <u>A</u>rithmetic mean) for generating a tree plot.</p>
<p>The following batch file will standardize a data matrix by rows, compute a variety of similarity and dissimilarity coefficients for the data matrix, perform clustering analysis using SAHN (<u>S</u>equential, <u>A</u>gglomerative, <u>H</u>ierarchical, and <u>N</u>ested clustering method) and UPGMA method, and display tree plot.</p>
<code style="font-size: small; color:blue;">*stand o=data.nts r=sdata.nts d=row<br/>
*simint o=sdata.nts r=dist.nts<br/>
*sahn o=dist.nts r=tree.nts cm=upgma<br/>
*tree o=tree.nts</code>
<p><a href="https://drive.google.com/uc?export=view&id=15eM_ktPYzxNRWnF6yG0unnbFrt3oPt_1" target="_blank"><img alt="Tree Plot" src="https://drive.google.com/uc?export=view&id=15eM_ktPYzxNRWnF6yG0unnbFrt3oPt_1" style="display: block; margin: 0 auto;" /></a></p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-87193006387847568752022-01-08T10:25:00.002+05:302022-01-08T10:44:59.171+05:30Benefits of Falling Lizard<img alt="Benefits of Falling Lizard" src="https://drive.google.com/uc?export=view&id=1nt3ipqIPEFGnR9JH5rIfuzyX04iruYYI" style="display: none;" />
<p style="display: none;">பல்லி விழும் பலன்கள். Benefits of falling lizard in human body parts.</p>
<table style='border-collapse:collapse;border:none;margin-left:auto;margin-right:auto'>
<tr>
<td width=436 colspan=3 style='width:327.35pt;border:double #33CC33 1.5pt;
background:#FF0066;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><b><span
style='font-size:14pt;color:white'>பல்லி
விழும் பலன்கள்</span></b></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border:double #33CC33 1.5pt;border-top:
none;background:yellow;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><b><span
style='color:#548235'>உறுப்பு</span></b></p>
</td>
<td width=145 style='width:109.1pt;border-top:none;border-left:none;
border-bottom:double #33CC33 1.5pt;border-right:double #33CC33 1.5pt;
background:yellow;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><b><span
style='color:#548235'>இடம்</span></b></p>
</td>
<td width=146 style='width:109.15pt;border-top:none;border-left:none;
border-bottom:double #33CC33 1.5pt;border-right:double #33CC33 1.5pt;
background:yellow;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><b><span
style='color:#548235'>வலம்</span></b></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FBE4D5;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>தலை</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>கலகம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>துன்பம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FBE4D5;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>வயிறு</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>தானியம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>மகிழ்ச்சி</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FBE4D5;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>கண்</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>சுகம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>சிறைபயம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FBE4D5;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>பிருஷ்டம்</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>சுகம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>செல்வம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FBE4D5;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>காது</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>ஆயுள்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>லாபம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FBE4D5;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>கணைக்கால்</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>பிரயாணம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
lang=TA style='color:#385723'>சுகம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FBE4D5;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>மணிக்கட்டு</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>பீடை</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>கீர்த்தி</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border:double #33CC33 1.5pt;border-top:
none;background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>நகம்</span></p>
</td>
<td width=145 style='width:109.1pt;border-top:none;border-left:none;
border-bottom:double #33CC33 1.5pt;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>செலவு</span></p>
</td>
<td width=146 style='width:109.15pt;border-top:none;border-left:none;
border-bottom:double #33CC33 1.5pt;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>நஷ்டம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#E2EFD9;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>மார்பு</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>தனலாபம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>சுகம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#E2EFD9;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>நெற்றி</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>லட்சுமிகரம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>காரியசித்தி</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#E2EFD9;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>முதுகு</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>நஷ்டம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>கவலை</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#E2EFD9;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>உதடு</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>கஷ்டம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>வரவு</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#E2EFD9;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>முழங்கால்</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>நஷ்டம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>பந்தயம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#E2EFD9;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>தோல்</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>வெற்றி</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>போகம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#E2EFD9;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>பாதவிரல்</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>ராசபயம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>நோய்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border:double #33CC33 1.5pt;border-top:
none;background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>கைவிரல்</span></p>
</td>
<td width=145 style='width:109.1pt;border-top:none;border-left:none;
border-bottom:double #33CC33 1.5pt;border-right:double #33CC33 1.5pt;
background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>சன்மானம்</span></p>
</td>
<td width=146 style='width:109.15pt;border-top:none;border-left:none;
border-bottom:double #33CC33 1.5pt;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>சஞ்சலம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FFF2CC;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>கபாலம்</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>கதனம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>வரவு</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FFF2CC;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>விலை</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>வாழ்வு</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>தாழ்வு</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FFF2CC;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>மூக்கு</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>வியாதி</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>கவலை</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FFF2CC;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>தொடை</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>துக்கம்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>சஞ்சலம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FFF2CC;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>கழுத்து</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>பகை</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>வெற்றி</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border-top:none;border-left:double #33CC33 1.5pt;
border-bottom:none;border-right:double #33CC33 1.5pt;background:#FFF2CC;
padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>பாதம்</span></p>
</td>
<td width=145 style='width:109.1pt;border:none;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>நோய்</span></p>
</td>
<td width=146 style='width:109.15pt;border:none;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>துக்கம்</span></p>
</td>
</tr>
<tr>
<td width=145 style='width:109.1pt;border:double #33CC33 1.5pt;border-top:
none;background:#FFF2CC;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#385723'>கை</span></p>
</td>
<td width=145 style='width:109.1pt;border-top:none;border-left:none;
border-bottom:double #33CC33 1.5pt;border-right:double #33CC33 1.5pt;
background:#FBE4D5;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:red'>துக்கம்</span></p>
</td>
<td width=146 style='width:109.15pt;border-top:none;border-left:none;
border-bottom:double #33CC33 1.5pt;border-right:double #33CC33 1.5pt;
background:#E2EFD9;padding:0in 5.4pt 0in 5.4pt'>
<p align=center style='margin-top:1.5pt;margin-right:0in;
margin-bottom:1.5pt;margin-left:0in;text-align:center;line-height:normal'><span
style='color:#1F4E79'>துன்பம்</span></p>
</td>
</tr>
</table>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-7098295892341089622021-06-08T20:33:00.021+05:302023-04-19T13:12:57.410+05:30TNEB Bill Calculator<img alt="TNEB" src="https://drive.google.com/uc?export=view&id=1NFjqYm5MUEHv6_XkLaYydPUuONO6omoL" style="display: none;" />
<p style="display: none;">நீங்கள் வீட்டில் இருந்தபடியே உங்கள் மின் உபயோக கட்டணத் தொகை சுலபமாக அறிந்து கொள்ளலாம்.</p>
<script type="text/javascript">
function calculateEB() {
var ebAmount = 0;
var tariff = 0;
var ebUnits = 0;
if ((document.getElementById("inputunits").value !== '') || (document.getElementById("inputunits").value > 0)) {
ebUnits = parseInt(document.getElementById('inputunits').value, 10);
if (ebUnits > 0 && ebUnits <= 100) {
ebAmount = ebUnits * 2.25;
tariff = 0;
} else if (ebUnits <= 200) {
ebAmount = (ebUnits - 100) * 2.25;
tariff = ebAmount;
} else if (ebUnits <= 400) {
ebAmount = 225 + ((ebUnits - 200) * 4.5);
tariff = ebAmount;
} else if (ebUnits <= 500) {
ebAmount = 1125 + ((ebUnits - 400) * 6);
tariff = ebAmount;
} else if (ebUnits <= 600) {
ebAmount = 1950 + ((ebUnits - 500) * 8);
tariff = ebAmount;
} else if (ebUnits <= 800) {
ebAmount = 2750 + ((ebUnits - 600) * 9);
tariff = ebAmount;
} else if (ebUnits <= 1000) {
ebAmount = 4550 + ((ebUnits - 800) * 10);
tariff = ebAmount;
} else if (ebUnits > 1000) {
ebAmount = 6550 + ((ebUnits - 1000) * 11);
tariff = ebAmount;
} else {
tariff = 0;
}
document.getElementById("info").innerHTML = "Bill Amount: <b style='background-color: #FFFF00; color:red;'>₹ " + tariff.toFixed(2) + "</b>";
} else {
document.getElementById("info").innerHTML = "<b style='background-color: #FFFF00; color:red;'>Please Enter a Valid Unit!</b>";
}
}
window.addEventListener('keyup', function(event) {
if (event.keyCode === 13) {
calculateEB();
}
});
</script>
<table border='0' height='100%' width='100%'>
<tr>
<td valign='middle'>
<p align="center"><font face="'Times New Roman', Times, Serif" size="4px" color="#336699"><b>TNEB Bill Calculator - 2022</b></font><br/><small>(Revised on September 09, 2022)</small>
</p>
<center>
<table align="center" bgcolor="navy" border="0" cellspacing="0" cellpadding="1">
<tr>
<td>
<table bgcolor="#CFCFF4" style="color: black; border: 1px solid #EEEEEE !important;" cellspacing="0" cellpadding="3" width="100%">
<tr>
<td align="center" style="font-family: 'Times New Roman', Times, Serif; font-size: 14px;">
<b>For Domestic Usage Only</b>
<div style="padding: 6px 0px 6px 0px;">Units Consumed:
<input type="number" style="outline: none;" id="inputunits" name="inputunits" min="1" oninput="validity.valid||(value='');" style="width: 90px;" autofocus required />
<input type="button" style="background-color:seablue; color:blue;" id="calculate" onclick="calculateEB()" value="Calculate" /></div>
<div id="info"></div>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>
<table summary="TANGEDCO April 2016 Tariffs" bgcolor="#CFCFF4" border="1" bordercolor="#eeeeee" cellspacing="0" cellpadding="3" width="100%" style="color: black; font-family: 'Times New Roman', Times, Serif; font-size: 14px;">
<tr style="text-align: center">
<th rowspan="2" style="text-align: center; border-right: 1px solid #000080 !important;">Units<br/>(<i>u</i>)</th>
<th rowspan="2" style="text-align: center; border-right: 1px solid #000080 !important;">Subsidy<br/>(≤ 100 <i>u</i>)</th>
<th colspan="2" style="text-align: center; border-right: 1px solid #000080 !important; border-bottom: 1px solid #000080 !important;">Unit Range</th>
<th rowspan="2">Unit<br/>Cost</th>
</tr>
<tr style="text-align: center; font-weight: bold">
<td style="text-align: center; border-right: 1px solid #000080 !important;">From</td>
<td style="text-align: center; border-right: 1px solid #000080 !important;">To</td>
</tr>
<! -- Upto 100 Units -->
<tr style="text-align: center; border-top: 1px solid #000080 !important;">
<td style="text-align: center; border-right: 1px solid #000080 !important;">≤ 100</td>
<td style="text-align: center; border-right: 1px solid #000080 !important;">₹ 4.50 × <i>u</i></td>
<td style="text-align: center; border-right: 1px solid #000080 !important;">1</td>
<td style="text-align: center; border-right: 1px solid #000080 !important;">100</td>
<td>₹ 0.00</td>
</tr>
<! -- Upto 200 Units -->
<tr style="text-align: center; border-top: 1px solid #000080 !important;">
<td rowspan="2" style="text-align: center; border-right: 1px solid #000080 !important;">≤ 200</td>
<td rowspan="2" style="text-align: center; border-right: 1px solid #000080 !important;">₹ 450</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">1</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">100</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 0.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-right: 1px solid #000080 !important;">101</td>
<td style="text-align: center; border-right: 1px solid #000080 !important;">200</td>
<td>₹ 2.25</td>
</tr>
<! -- Upto 400 Units -->
<tr style="text-align: center; border-top: 1px solid #000080 !important;">
<td rowspan="3" style="text-align: center; border-right: 1px solid #000080 !important;">≤ 400</td>
<td rowspan="3" style="text-align: center; border-right: 1px solid #000080 !important;">₹ 450</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">1</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">100</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 0.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">101</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">200</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 2.25</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-right: 1px solid #000080 !important;">201</td>
<td style="text-align: center; border-right: 1px solid #000080 !important;">400</td>
<td>₹ 4.50</td>
</tr>
<! -- Upto 500 Units -->
<tr style="text-align: center; border-top: 1px solid #000080 !important;">
<td rowspan="4" style="text-align: center; border-right: 1px solid #000080 !important;">≤ 500</td>
<td rowspan="4" style="text-align: center; border-right: 1px solid #000080 !important;">₹ 450</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">1</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">100</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 0.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">101</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">200</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 2.25</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">201</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">400</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 4.50</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-right: 1px solid #000080 !important;">401</td>
<td style="text-align: center; border-right: 1px solid #000080 !important;">500</td>
<td>₹ 6.00</td>
</tr>
<! -- Upto 600 Units -->
<tr style="text-align: center; border-top: 1px solid #000080 !important;">
<td rowspan="4" style="text-align: center; border-right: 1px solid #000080 !important;">≤ 600</td>
<td rowspan="4" style="text-align: center; border-right: 1px solid #000080 !important;">₹ 450</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">1</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">100</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 0.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">101</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">400</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 4.50</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">401</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">500</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 6.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-right: 1px solid #000080 !important;">501</td>
<td style="text-align: center; border-right: 1px solid #000080 !important;">600</td>
<td>₹ 8.00</td>
</tr>
<! -- Upto 800 Units -->
<tr style="text-align: center; border-top: 1px solid #000080 !important;">
<td rowspan="5" style="text-align: center; border-right: 1px solid #000080 !important;">≤ 800</td>
<td rowspan="5" style="text-align: center; border-right: 1px solid #000080 !important;">₹ 450</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">1</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">100</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 0.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">101</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">400</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 4.50</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">401</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">500</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 6.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">501</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">600</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 8.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-right: 1px solid #000080 !important;">601</td>
<td style="text-align: center; border-right: 1px solid #000080 !important;">800</td>
<td>₹ 9.00</td>
</tr>
<! -- Upto 1000 Units -->
<tr style="text-align: center; border-top: 1px solid #000080 !important;">
<td rowspan="6" style="text-align: center; border-right: 1px solid #000080 !important;">≤ 1000</td>
<td rowspan="6" style="text-align: center; border-right: 1px solid #000080 !important;">₹ 450</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">1</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">100</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 0.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">101</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">400</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 4.50</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">401</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">500</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 6.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">501</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">600</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 8.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">601</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">800</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 9.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-right: 1px solid #000080 !important;">801</td>
<td style="text-align: center; border-right: 1px solid #000080 !important;">1000</td>
<td>₹ 10.00</td>
</tr>
<! -- Above 1000 Units -->
<tr style="text-align: center; border-top: 1px solid #000080 !important;">
<td rowspan="7" style="text-align: center; border-right: 1px solid #000080 !important;">> 1000</td>
<td rowspan="7" style="text-align: center; border-right: 1px solid #000080 !important;">₹ 450</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">1</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">100</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 0.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">101</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">400</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 4.50</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">401</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">500</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 6.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">501</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">600</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 8.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">601</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">800</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 9.00</td>
</tr>
<tr style="text-align: center;">
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">801</td>
<td style="text-align: center; border-bottom: 1px solid #000080 !important; border-right: 1px solid #000080 !important;">1000</td>
<td style="border-bottom: 1px solid #000080 !important;">₹ 10.00</td>
</tr>
<tr style="text-align: center;">
<td colspan="2" style="text-align: center; border-right: 1px solid #000080 !important;">> 1000</td>
<td>₹ 11.00</td>
</tr>
</table>
</td>
</tr>
</table>
</center>
</td>
</tr>
</table>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com59tag:blogger.com,1999:blog-1315445647083902393.post-72698500454096466862021-04-15T13:49:00.000+05:302021-04-15T13:49:40.608+05:30RNA-RNA Interaction Prediction and Visualization<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<p><a href="https://drive.google.com/uc?export=view&id=1-8z8-5lgWb6DCNbHsWkAcWOIVo8zvADW" target="_blank"><img alt="RactIP" src="https://drive.google.com/uc?export=view&id=1-8z8-5lgWb6DCNbHsWkAcWOIVo8zvADW" style="display: block; margin: 0 auto; padding-bottom: 20px;" /></a></p>
<p>Ribonucleic acid (RNA) is a linear polymeric molecule composed of four bases namely adenine (A), cytosine (C), guanine (G), and uracil (U). It is used for the prediction of various functions which include coding, decoding, regulation, and gene expression. The prediction of RNA–RNA interaction plays a major role in the study of structure folding and free energy of RNA complex molecule. This is a video tutorial for RNA-RNA interaction prediction using RactIP (RNA-RNA interACTion prediction using IP) and visualize inter and/or intramolecular base-pair interactions using VARNA (Visualization Applet for RNA) tools. The list of tools used is <a href="http://rtips.dna.bio.keio.ac.jp/ractip/" target="_blank">RactIP</a> and <a href="http://varna.lri.fr/" target="_blank">VARNA</a>.</p>
<p style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="270" width="480" src="https://www.youtube.com/embed/9eqzJ2iaERo"></iframe>
</p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-92077687830139998472021-02-11T21:09:00.000+05:302021-02-11T21:15:43.352+05:30Best Fonts to Display Biological Sequence and Alignment<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1OwMAaKUHCGkTjwNO2hiMOldBN_gacLwv" target="_blank"><img alt="FASTA Sequence" src="https://drive.google.com/uc?export=view&id=1OwMAaKUHCGkTjwNO2hiMOldBN_gacLwv" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a><br />
<p>Biological sequence alignment is a method to find similarities between two sequences. The characters (letters or biological sequence alphabets) are arranged row-wise and column-wise according to match/identity and mismatch of characters through symbol representation. In row-wise, a gap character (hyphen symbol ‘-’) is used to align/adjust the sequence characters for matching without changing the order. Correspondingly, the column-wise characters such as match (same character, pipe symbol ‘|’, colon symbol ‘:’, asterisk symbol ‘*’, or dot symbol ‘.’), mismatch (anyone of the sequence character, or blank space ‘ ’), positive (positive symbol ‘+’), and gap/indel (blank space ‘ ’) are used to represent sequence alignment.</p>
<p>A sequence or sequence alignment must be properly formatted in a text editor/word processor using fixed-width fonts to find the differences of characters in the sequence and control word wrapping. Formatting sequence helps to find the sequence length and formatting sequence alignment helps to find the sequence similarity. There are many fixed-width fonts (<i>a.k.a.</i> monospaced font, non-proportional font, or fixed-pitch) that occupy equal width for each character useful for arranging the characters. The most commonly used fixed-width fonts that come by default with the system (varies in different OS) are <i>Courier New</i>, <i>Consolas</i>, <i>Lucida Sans Typewriter</i>, and <i>Monaco</i>. There are many types of fixed-width fonts can be freely downloaded from <a href="https://fonts.google.com/?category=Monospace" target="_blank">Google Fonts</a>, <a href="https://www.1001freefonts.com/fixed-width-fonts.php" target="_blank">1001 Free Fonts</a>, <a href="https://www.fontsquirrel.com/fonts/list/classification/monospaced" target="_blank">Font Squirrel</a>, <a href="https://www.fontspace.com/search?q=monospace" target="_blank">FontSpace</a>, etc. A perfect example for formatted pairwise and multiple sequence alignment is below.</p>
<a href="https://drive.google.com/uc?export=view&id=1Nf2u9DQWW1XpTWFj0r1JfLfiNgdYvHQj" target="_blank"><img alt="Sequence Alignments" src="https://drive.google.com/uc?export=view&id=1Nf2u9DQWW1XpTWFj0r1JfLfiNgdYvHQj" style="display: block; margin: 0 auto; padding-top: 10px;" /></a>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-78009904698096848712020-12-04T15:59:00.001+05:302020-12-04T15:59:59.890+05:30Creating Custom Database using Standalone NCBI BLAST+<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<a href="https://drive.google.com/uc?export=view&id=1yX2XkZtH0OZJlUDyFLb1BuTtbbCHS0N6" target="_blank"><img alt="NCBI BLAST+" src="https://drive.google.com/uc?export=view&id=1yX2XkZtH0OZJlUDyFLb1BuTtbbCHS0N6" style="display: block; margin: 0 auto; padding-bottom: 10px;" /></a><br />
<p>Basic Local Alignment Search Tool (BLAST) is a collection of programs developed using heuristic algorithm in C++ for comparing DNA, RNA, and protein sequences. The standalone command-line interface (CLI) of BLAST is named as BLAST+. The latest version of NCBI BLAST+ can be downloaded from the FTP server of NCBI (<a href="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST" target="_blank">ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST</a>). This is a simple tutorial for creating a custom database, accessing the database, and performing a sequence search using BLAST+.</p>
<h3 style="color: blue">1. Creating a Custom Database</h3>
<p>A nucleotide (<small><code>nucl</code></small>) or protein (<small><code>prot</code></small>) database can be created using <small><code>-dbtype</code></small> parameter in <small><code>makeblastdb</code></small> program. We can create two types of database using command-line below,</p>
<p><b>Non-indexed Database:</b> <small><code>./makeblastdb -in DBX.fasta -out DBX -dbtype prot</code></small></p>
<pre><small>Building a new DB, current time: 12/04/2020 10:10:06
New DB name: C:\NCBI\blast-2.6.0+\bin\DBX
New DB title: DBX.fasta
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 20 sequences in 0.0041614 seconds.</small></pre>
<p><b>Indexed Database:</b> <small><code>./makeblastdb -in DB.fasta -out DB -dbtype prot -parse_seqids</code></small></p>
<pre><small>Building a new DB, current time: 12/03/2020 17:29:38
New DB name: C:\NCBI\blast-2.11.0+\bin\DB
New DB title: DB.fasta
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 20 sequences in 0.0277056 seconds.</small></pre>
<p>The sequence files <b>DB.fasta</b> and <b>DBX.fasta</b> were given at end of this page.</p>
<h3 style="color: blue">2. List of Records in the Database</h3>
<p>List of entries in the database can be viewed using <small><code>-entry all</code></small> parameter in <small><code>blastdbcmd</code></small> program. The command-line to get the list of sequence identifiers assigned to the non-indexed and indexed database are below,</p>
<p><b>Non-indexed Database:</b> <small><code>./blastdbcmd -db DBX -entry all -outfmt "OID: %o GI: %g ACC: %a IDENTIFIER: %i"</code></small></p>
<pre><small>OID: 0 GI: N/A ACC: BL_ORD_ID:0 IDENTIFIER: gnl|BL_ORD_ID|0
OID: 1 GI: N/A ACC: BL_ORD_ID:1 IDENTIFIER: gnl|BL_ORD_ID|1
OID: 2 GI: N/A ACC: BL_ORD_ID:2 IDENTIFIER: gnl|BL_ORD_ID|2
OID: 3 GI: N/A ACC: BL_ORD_ID:3 IDENTIFIER: gnl|BL_ORD_ID|3
OID: 4 GI: N/A ACC: BL_ORD_ID:4 IDENTIFIER: gnl|BL_ORD_ID|4
OID: 5 GI: N/A ACC: BL_ORD_ID:5 IDENTIFIER: gnl|BL_ORD_ID|5
OID: 6 GI: N/A ACC: BL_ORD_ID:6 IDENTIFIER: gnl|BL_ORD_ID|6
OID: 7 GI: N/A ACC: BL_ORD_ID:7 IDENTIFIER: gnl|BL_ORD_ID|7
OID: 8 GI: N/A ACC: BL_ORD_ID:8 IDENTIFIER: gnl|BL_ORD_ID|8
OID: 9 GI: N/A ACC: BL_ORD_ID:9 IDENTIFIER: gnl|BL_ORD_ID|9
OID: 10 GI: N/A ACC: BL_ORD_ID:10 IDENTIFIER: gnl|BL_ORD_ID|10
OID: 11 GI: N/A ACC: BL_ORD_ID:11 IDENTIFIER: gnl|BL_ORD_ID|11
OID: 12 GI: N/A ACC: BL_ORD_ID:12 IDENTIFIER: gnl|BL_ORD_ID|12
OID: 13 GI: N/A ACC: BL_ORD_ID:13 IDENTIFIER: gnl|BL_ORD_ID|13
OID: 14 GI: N/A ACC: BL_ORD_ID:14 IDENTIFIER: gnl|BL_ORD_ID|14
OID: 15 GI: N/A ACC: BL_ORD_ID:15 IDENTIFIER: gnl|BL_ORD_ID|15
OID: 16 GI: N/A ACC: BL_ORD_ID:16 IDENTIFIER: gnl|BL_ORD_ID|16
OID: 17 GI: N/A ACC: BL_ORD_ID:17 IDENTIFIER: gnl|BL_ORD_ID|17
OID: 18 GI: N/A ACC: BL_ORD_ID:18 IDENTIFIER: gnl|BL_ORD_ID|18
OID: 19 GI: N/A ACC: BL_ORD_ID:19 IDENTIFIER: gnl|BL_ORD_ID|19</small></pre>
<p><b>Indexed Database:</b> <small><code>./blastdbcmd -db DB -entry all -outfmt "OID: %o GI: %g ACC: %a IDENTIFIER: %i"</code></small></p>
<pre><small>OID: 0 GI: N/A ACC: Sequence1 IDENTIFIER: lcl|Sequence1
OID: 1 GI: N/A ACC: Sequence2 IDENTIFIER: lcl|Sequence2
OID: 2 GI: N/A ACC: Sequence3 IDENTIFIER: lcl|Sequence3
OID: 3 GI: N/A ACC: Sequence4 IDENTIFIER: lcl|Sequence4
OID: 4 GI: N/A ACC: Sequence5 IDENTIFIER: lcl|Sequence5
OID: 5 GI: N/A ACC: Sequence6 IDENTIFIER: lcl|Sequence6
OID: 6 GI: N/A ACC: Sequence7 IDENTIFIER: lcl|Sequence7
OID: 7 GI: N/A ACC: Sequence8 IDENTIFIER: lcl|Sequence8
OID: 8 GI: N/A ACC: Sequence9 IDENTIFIER: lcl|Sequence9
OID: 9 GI: N/A ACC: Sequence10 IDENTIFIER: lcl|Sequence10
OID: 10 GI: N/A ACC: Sequence11 IDENTIFIER: lcl|Sequence11
OID: 11 GI: N/A ACC: Sequence12 IDENTIFIER: lcl|Sequence12
OID: 12 GI: N/A ACC: Sequence13 IDENTIFIER: lcl|Sequence13
OID: 13 GI: N/A ACC: Sequence14 IDENTIFIER: lcl|Sequence14
OID: 14 GI: N/A ACC: Sequence15 IDENTIFIER: lcl|Sequence15
OID: 15 GI: N/A ACC: Sequence16 IDENTIFIER: lcl|Sequence16
OID: 16 GI: N/A ACC: Sequence17 IDENTIFIER: lcl|Sequence17
OID: 17 GI: N/A ACC: Sequence18 IDENTIFIER: lcl|Sequence18
OID: 18 GI: N/A ACC: Sequence19 IDENTIFIER: lcl|Sequence19
OID: 19 GI: N/A ACC: Sequence20 IDENTIFIER: lcl|Sequence20</small></pre>
<p>The identifier <i>BLAST Ordinal Identifiers</i> (BL_ORD_ID) and <i>General</i> (GNL) represents non-indexed database and <i>Local</i> (LCL) represents indexed database.</p>
<h3 style="color: blue">3. Searching Sequence from the Database</h3>
<p>Sequence in the database can be accessed through entry ID using <small><code>-entry</code></small> parameter in <small><code>blastdbcmd</code></small> program. The command-line to access entry from the non-indexed and indexed database are below,</p>
<p><b>Non-indexed Database:</b> <small><code>./blastdbcmd -db DBX -entry 'gnl|BL_ORD_ID|1'</code></small></p>
<pre><small>>AAA40590.1 insulin [Octodon degus]
MAPWMHLLTVLALLALWGPNSVQAYSSQHLCGSNLVEALYMTCGRSGFYRPHDRRELEDLQVEQAELGLEAGGLQPSALE
MILQKRGIVDQCCNNICTFNQLQNYCNVP</small></pre>
<p>The latest BLAST+ does not permit access to first entry (index number ‘0’) in the non-indexed database; since the starting index number is ‘1’. Moreover, it does not recognize entries of a non-indexed database. I have used BLAST+ version 2.6.0 to construct a non-indexed database.</p>
<pre><small>./blastdbcmd -db DBX -entry 'gnl|BL_ORD_ID|0'
Error: [blastdbcmd] CObject_id::GetId(): Invalid choice selection: NCBI-General::Object-id.str</small></pre>
<p><b>Indexed Database:</b> <small><code>./blastdbcmd -db DB -entry Sequence1</code></small></p>
<pre><small>Sequence1 NP_001191615.1 insulin precursor [Aplysia californica]
MSKFLLQSHSANACLLTLLLTLASNLDISLANFEHSCNGYMRPHPRGLCGEDLHVIISNLCSSLGGNRRFLAKYMVKRDT
ENVNDKLRGILLNKKEAFSYLTKREASGSITCECCFNQCRIFELAQYCRLPDHFFSRISRTGRSNSGHAQLEDNFS</small></pre>
<h3 style="color: blue">4. Retrieving Sequence from the Database</h3>
<p>Sequence from the database can be retrieved through entry ID using <small><code>-entry</code></small> parameter in <small><code>blastdbcmd</code></small> program. The command-line to retrieve the sequence to file from the non-indexed and indexed database are below,</p>
<p><b>Non-indexed Database:</b> <small><code>./blastdbcmd -db DBX -entry 'gnl|BL_ORD_ID|1' -out Sequence2.fasta</code></small></p>
<p><b>Indexed Database:</b> <small><code>./blastdbcmd -db DB -entry Sequence1 -out Sequence1.fasta</code></small></p>
<h3 style="color: blue">5. Performing Pairwise Alignment</h3>
<p>Pairwise sequence alignment can be performed be passing query as a input file (in fasta file format) through parameters, or raw sequence (not supported in BLAST+ old versions) through command-line. The command-line to perform pairwise alignment are below,</p>
<p><small><code>./blastp -db DB -query sequence.fasta</code></small>, OR</p>
<p><small><code>echo ALLALLALGAPTPARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVE | ./blastp -db DB</code></small></p>
<p>The sequence alignment output is below,</p>
<pre style="font-size: small; font-famil: monospace;">BLASTP 2.11.0+
Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.
Reference for composition-based statistics: Alejandro A. Schaffer,
L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri
I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
"Improving the accuracy of PSI-BLAST protein database searches with
composition-based statistics and other refinements", Nucleic Acids
Res. 29:2994-3005.
Database: DB.fasta
20 sequences; 2,178 total letters
Query=
Length=59
Score E
Sequences producing significant alignments: (Bits) Value
Sequence3 KAB1251309.1 Insulin [Camelus dromedarius] 120 3e-41
Sequence16 AAA59172.1 insulin [Homo sapiens] 91.3 6e-30
Sequence10 AAA19033.1 insulin [Oryctolagus cuniculus] 89.7 3e-29
Sequence4 NP_001035835.1 insulin, isoform 2 precursor [Homo sapiens] 85.1 2e-26
Sequence8 AAB60625.1 insulin [Ovis aries] 82.0 2e-26
Sequence20 ELK28555.1 Insulin [Myotis davidii] 77.0 1e-23
Sequence7 pir||INHY insulin - hamster 65.5 3e-20
Sequence13 pir||INEL insulin - elephant 64.7 6e-20
Sequence15 pir||INTK insulin - turkey (tentative sequence) 63.5 1e-19
Sequence12 pir||INOS insulin - ostrich 63.5 1e-19
Sequence11 pir||INMKSQ insulin - common squirrel monkey 60.1 3e-18
Sequence2 AAA40590.1 insulin [Octodon degus] 60.8 6e-18
Sequence6 pir||INCD insulin - cod (Gadus sp.) 55.8 2e-16
Sequence5 NP_571131.1 insulin preproprotein [Danio rerio] 53.9 3e-15
Sequence9 XP_014388588.1 PREDICTED: insulin [Myotis brandtii] 48.9 1e-12
Sequence19 BAS32722.1 insulin, partial [Varanus exanthematicus] 38.5 2e-09
Sequence17 QBX89050.1 insulin, partial [Nephrops norvegicus] 19.6 0.042
>Sequence3 KAB1251309.1 Insulin [Camelus dromedarius]
Length=110
Score = 120 bits (300), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 59/59 (100%), Positives = 59/59 (100%), Gaps = 0/59 (0%)
Query 1 ALLALLALGAPTPARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVE 59
ALLALLALGAPTPARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVE
Sbjct 9 ALLALLALGAPTPARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVE 67
>Sequence16 AAA59172.1 insulin [Homo sapiens]
Length=110
Score = 91.3 bits (225), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 42/50 (84%), Positives = 42/50 (84%), Gaps = 0/50 (0%)
Query 10 APTPARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVE 59
P PA AF NQHLCGSHLVEALYLVCGERGFFYTPK RRE ED QVG VE
Sbjct 18 GPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVE 67
>Sequence10 AAA19033.1 insulin [Oryctolagus cuniculus]
Length=110
Score = 89.7 bits (221), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 40/47 (85%), Positives = 43/47 (91%), Gaps = 0/47 (0%)
Query 13 PARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVE 59
PA+AF NQHLCGSHLVEALYLVCGERGFFYTPK+RREVE+ QVG E
Sbjct 21 PAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKSRREVEELQVGQAE 67
>Sequence4 NP_001035835.1 insulin, isoform 2 precursor [Homo sapiens]
Length=200
Score = 85.1 bits (209), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 38/44 (86%), Positives = 38/44 (86%), Gaps = 0/44 (0%)
Query 11 PTPARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQ 54
P PA AF NQHLCGSHLVEALYLVCGERGFFYTPK RRE ED Q
Sbjct 19 PDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQ 62
>Sequence8 AAB60625.1 insulin [Ovis aries]
Length=105
Score = 82.0 bits (201), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 38/43 (88%), Positives = 39/43 (91%), Gaps = 0/43 (0%)
Query 16 AFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGV 58
AF NQHLCGSHLVEALYLVCGERGFFYTPKARREVE QVG +
Sbjct 24 AFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVEGPQVGAL 66
>Sequence20 ELK28555.1 Insulin [Myotis davidii]
Length=168
Score = 77.0 bits (188), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 34/40 (85%), Positives = 36/40 (90%), Gaps = 0/40 (0%)
Query 15 RAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQ 54
+AF NQHLCGSHLVEALYLVCGERGFFYTPK RRE+ D Q
Sbjct 23 QAFVNQHLCGSHLVEALYLVCGERGFFYTPKDRRELPDPQ 62
Score = 44.3 bits (103), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 24/52 (46%), Positives = 32/52 (62%), Gaps = 2/52 (4%)
Query 8 LGAPTPARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVE 59
L + P+++ +QHLCG LV AL + CG+RG FY P A E +D Q VE
Sbjct 80 LASVDPSQS-QDQHLCGDELVNALTITCGDRG-FYNPMAPLEQDDLQEEEVE 129
>Sequence7 pir||INHY insulin - hamster
Length=51
Score = 65.5 bits (158), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 28/30 (93%), Positives = 29/30 (97%), Gaps = 0/30 (0%)
Query 17 FANQHLCGSHLVEALYLVCGERGFFYTPKA 46
F NQHLCGSHLVEALYLVCGERGFFYTPK+
Sbjct 1 FVNQHLCGSHLVEALYLVCGERGFFYTPKS 30
>Sequence13 pir||INEL insulin - elephant
Length=51
Score = 64.7 bits (156), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 28/30 (93%), Positives = 28/30 (93%), Gaps = 0/30 (0%)
Query 17 FANQHLCGSHLVEALYLVCGERGFFYTPKA 46
F NQHLCGSHLVEALYLVCGERGFFYTPK
Sbjct 1 FVNQHLCGSHLVEALYLVCGERGFFYTPKT 30
>Sequence15 pir||INTK insulin - turkey (tentative sequence)
Length=51
Score = 63.5 bits (153), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 28/29 (97%), Positives = 29/29 (100%), Gaps = 0/29 (0%)
Query 18 ANQHLCGSHLVEALYLVCGERGFFYTPKA 46
ANQHLCGSHLVEALYLVCGERGFFY+PKA
Sbjct 2 ANQHLCGSHLVEALYLVCGERGFFYSPKA 30
>Sequence12 pir||INOS insulin - ostrich
Length=51
Score = 63.5 bits (153), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 28/29 (97%), Positives = 29/29 (100%), Gaps = 0/29 (0%)
Query 18 ANQHLCGSHLVEALYLVCGERGFFYTPKA 46
ANQHLCGSHLVEALYLVCGERGFFY+PKA
Sbjct 2 ANQHLCGSHLVEALYLVCGERGFFYSPKA 30
>Sequence11 pir||INMKSQ insulin - common squirrel monkey
Length=51
Score = 60.1 bits (144), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 26/30 (87%), Positives = 26/30 (87%), Gaps = 0/30 (0%)
Query 17 FANQHLCGSHLVEALYLVCGERGFFYTPKA 46
F NQHLCG HLVEALYLVCGERGFFY PK
Sbjct 1 FVNQHLCGPHLVEALYLVCGERGFFYAPKT 30
>Sequence2 AAA40590.1 insulin [Octodon degus]
Length=109
Score = 60.8 bits (146), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 28/49 (57%), Positives = 35/49 (71%), Gaps = 1/49 (2%)
Query 11 PTPARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVE 59
P +A+++QHLCGS+LVEALY+ CG G FY P RRE+ED QV E
Sbjct 19 PNSVQAYSSQHLCGSNLVEALYMTCGRSG-FYRPHDRRELEDLQVEQAE 66
>Sequence6 pir||INCD insulin - cod (Gadus sp.)
Length=51
Score = 55.8 bits (133), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 23/27 (85%), Positives = 25/27 (93%), Gaps = 0/27 (0%)
Query 20 QHLCGSHLVEALYLVCGERGFFYTPKA 46
QHLCGSHLV+ALYLVCG+RGFFY PK
Sbjct 5 QHLCGSHLVDALYLVCGDRGFFYNPKG 31
>Sequence5 NP_571131.1 insulin preproprotein [Danio rerio]
Length=108
Score = 53.9 bits (128), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 25/32 (78%), Positives = 27/32 (84%), Gaps = 2/32 (6%)
Query 20 QHLCGSHLVEALYLVCGERGFFYTPKARREVE 51
QHLCGSHLV+ALYLVCG GFFY PK R+VE
Sbjct 27 QHLCGSHLVDALYLVCGPTGFFYNPK--RDVE 56
>Sequence9 XP_014388588.1 PREDICTED: insulin [Myotis brandtii]
Length=183
Score = 48.9 bits (115), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 26/51 (51%), Positives = 34/51 (67%), Gaps = 1/51 (2%)
Query 9 GAPTPARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVE 59
APTPA+AF +HLC L E L ++CG++G F PKA RE+ D Q G V+
Sbjct 17 WAPTPAQAFYFEHLCDEDLAEMLTIICGDQG-FRNPKATRELPDPQEGEVD 66
Score = 46.6 bits (109), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 22/40 (55%), Positives = 28/40 (70%), Gaps = 1/40 (3%)
Query 20 QHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVE 59
Q LCG LV+ L +VCG+RG FY+P A RE+ D Q G V+
Sbjct 106 QRLCGEDLVDTLTMVCGDRG-FYSPTALRELPDPQEGEVD 144
>Sequence19 BAS32722.1 insulin, partial [Varanus exanthematicus]
Length=88
Score = 38.5 bits (88), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 22/49 (45%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query 3 LALLALGAPTPARAFA--NQHLCGSHLVEALYLVCGERGFFYTPKARRE 49
L LLA+ APT A + ++HLCGS LVEAL CG+ G + K +
Sbjct 1 LVLLAVLAPTAIYATSENDEHLCGSALVEALVSACGKEGIYSFTKRNEQ 49
>Sequence17 QBX89050.1 insulin, partial [Nephrops norvegicus]
Length=178
Score = 19.6 bits (39), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query 20 QHLCGSHLVEALYLVCGERGFFYTP 44
+ LCG L L VC +G + P
Sbjct 25 RRLCGWRLANKLNRVC--KGVYNNP 47
Score = 13.1 bits (22), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 6/19 (32%), Positives = 7/19 (37%), Gaps = 0/19 (0%)
Query 32 YLVCGERGFFYTPKARREV 50
YL +R TP E
Sbjct 90 YLTFSQRASEDTPSEENEA 108
Lambda K H a alpha
0.324 0.139 0.423 0.792 4.96
Gapped
Lambda K H a alpha sigma
0.267 0.0410 0.140 1.90 42.6 43.6
Effective search space used: 57052
Database: DB.fasta
Posted date: Dec 3, 2020 5:29 PM
Number of letters in database: 2,178
Number of sequences in database: 20
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40</pre>
<h3 style="color: blue">6. Storing Pairwise Alignment Result</h3>
<p>The output of pairwise alignment can be stored to the local disk using command-line below,</p>
<p><small><code>./blastp -db DB -query sequence.fasta -outfmt 0 -out output.html -html</code></small></p>
<p>The list of sequence alignment output formats (<small><code>-outfmt</code></small>) are:</p>
<p><b>0</b> = Pairwise,<br>
<b>1</b> = Query-anchored showing identities,<br>
<b>2</b> = Query-anchored no identities,<br>
<b>3</b> = Flat query-anchored showing identities,<br>
<b>4</b> = Flat query-anchored no identities,<br>
<b>5</b> = BLAST XML,<br>
<b>6</b> = Tabular,<br>
<b>7</b> = Tabular with comment lines,<br>
<b>8</b> = Seqalign (Text ASN.1),<br>
<b>9</b> = Seqalign (Binary ASN.1),<br>
<b>10</b> = Comma-separated values,<br>
<b>11</b> = BLAST archive (ASN.1),<br>
<b>12</b> = Seqalign (JSON),<br>
<b>13</b> = Multiple-file BLAST JSON,<br>
<b>14</b> = Multiple-file BLAST XML2,<br>
<b>15</b> = Single-file BLAST JSON,<br>
<b>16</b> = Single-file BLAST XML2,<br>
<b>17</b> = Sequence Alignment/Map (SAM), and<br>
<b>18</b> = Organism Report</p>
<h3 style="color: red;">Sequence Files used for Database Creation</h3>
<p>The FASTA file formatted multiple sequence file (<b>DB.fasta</b>) is given below:</p>
<pre style="font-size: small; font-famil: monospace;">>Sequence1 NP_001191615.1 insulin precursor [Aplysia californica]
MSKFLLQSHSANACLLTLLLTLASNLDISLANFEHSCNGYMRPHPRGLCGEDLHVIISNLCSSLGGNRRF
LAKYMVKRDTENVNDKLRGILLNKKEAFSYLTKREASGSITCECCFNQCRIFELAQYCRLPDHFFSRISR
TGRSNSGHAQLEDNFS
>Sequence2 AAA40590.1 insulin [Octodon degus]
MAPWMHLLTVLALLALWGPNSVQAYSSQHLCGSNLVEALYMTCGRSGFYRPHDRRELEDLQVEQAELGLE
AGGLQPSALEMILQKRGIVDQCCNNICTFNQLQNYCNVP
>Sequence3 KAB1251309.1 Insulin [Camelus dromedarius]
MALWTRLLALLALLALGAPTPARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVELGG
GPGAGGLQPLGPEGRPQKRGIVEQCCASVCSLYQLENYCN
>Sequence4 NP_001035835.1 insulin, isoform 2 precursor [Homo sapiens]
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQASALSLSS
STSTWPEGLDATARAPPALVVTANIGQAGGSSSRQFRQRALGTSDSPVLFIHCPGAAGTAQGLEYRGRRV
TTELVWEEVDSSPQPQGSESLPAQPPAQPAPQPEPQQAREPSPEVSCCGLWPRRPQRSQN
>Sequence5 NP_571131.1 insulin preproprotein [Danio rerio]
MAVWLQAGALLVLLVVSSVSTNPGTPQHLCGSHLVDALYLVCGPTGFFYNPKRDVEPLLGFLPPKSAQET
EVADFAFKDHAELIRKRGIVEQCCHKPCSIFELQNYCN
>Sequence6 pir||INCD insulin - cod (Gadus sp.)
MAPPQHLCGSHLVDALYLVCGDRGFFYNPKGIVDQCCHRPCDIFDLQNYCN
>Sequence7 pir||INHY insulin - hamster
FVNQHLCGSHLVEALYLVCGERGFFYTPKSGIVDQCCTSICSLYQLENYCN
>Sequence8 AAB60625.1 insulin [Ovis aries]
MALWTRLVPLLALLALWAPAPAHAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVEGPQVGALELAG
GPGAGGLEGPPQKRGIVEQCCAGVCSLYQLENYCN
>Sequence9 XP_014388588.1 PREDICTED: insulin [Myotis brandtii]
MALWTRLLPLLALLALWAPTPAQAFYFEHLCDEDLAEMLTIICGDQGFRNPKATRELPDPQEGEVDMGAG
GQKALTLEQLLQNSDIPARLLALWAPAPAPAQSGEQRLCGEDLVDTLTMVCGDRGFYSPTALRELPDPQE
GEVDMGAGGQKALTLEQLLQNSDIVDMCCNNFCSFYQLEYYCN
>Sequence10 AAA19033.1 insulin [Oryctolagus cuniculus]
MASLAALLPLLALLVLCRLDPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKSRREVEELQVGQAELGG
GPGAGGLQPSALELALQKRGIVEQCCTSICSLYQLENYCN
>Sequence11 pir||INMKSQ insulin - common squirrel monkey
FVNQHLCGPHLVEALYLVCGERGFFYAPKTGVVDQCCTSICSLYQLQNYCN
>Sequence12 pir||INOS insulin - ostrich
AANQHLCGSHLVEALYLVCGERGFFYSPKAGIVEQCCHNTCSLYQLENYCN
>Sequence13 pir||INEL insulin - elephant
FVNQHLCGSHLVEALYLVCGERGFFYTPKTGIVEQCCTGVCSLYQLENYCN
>Sequence14 AAF80383.1 insulin precursor [Aplysia californica]
MSKFLLQSHSANACLLTLLLTLASNLDISLANFEHSCNGYMRPHPRGLCGEDLHVIISNLCSSLGGNRRF
LAKYMVKRDTENVNDKLRGILLNKKEAFSYLTKREASGSITCECCFNQCRIFELAQYCRLPDHFFSRISR
TGRSNSGHAQLEDNFS
>Sequence15 pir||INTK insulin - turkey (tentative sequence)
AANQHLCGSHLVEALYLVCGERGFFYSPKAGIVEQCCHNTCSLYQLENYCN
>Sequence16 AAA59172.1 insulin [Homo sapiens]
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG
GPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
>Sequence17 QBX89050.1 insulin, partial [Nephrops norvegicus]
VVVVVVGSSRASRRTYPTSEEEPRRRLCGWRLANKLNRVCKGVYNNPGSTGNYLFYRSRRDGESEPGLPP
EEYLDLLPDPEEERGLRHHYLTFSQRASEDTPSEENEAPGSFFGSLSPQDSPHQSAVQEDEASSVQFPFL
TEEEASQMVRVRPRSKRGLSAECCRKVCTVSELVGYCY
>Sequence18 ACQ91106.1 insulin, partial [Haliotis corrugata]
DLHVIISNLCSSLGGNRRFLAKYMVKRDTENVNDKLRGILLNKKEAFSYLTKREASGSITCECCFNQCRI
FELAQYCRLPDHFFSRISRTG
>Sequence19 BAS32722.1 insulin, partial [Varanus exanthematicus]
LVLLAVLAPTAIYATSENDEHLCGSALVEALVSACGKEGIYSFTKRNEQSLGHGLLDNEVPFHLGKRGIV
EDCCENICPWSVLQSYCR
>Sequence20 ELK28555.1 Insulin [Myotis davidii]
MALWTRLLPLLALLALWAPAPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKDRRELPDPQGESSPLTP
RSHPKGTGYLASVDPSQSQDQHLCGDELVNALTITCGDRGFYNPMAPLEQDDLQEEEVEMDEGGLQALTL
EGLLQKRGIVEECCTNVCSLYQLERYCN</pre>
The FASTA file formatted multiple sequence file (<b>DBX.fasta</b>) is given below:
<pre style="font-size: small; font-famil: monospace;">>NP_001191615.1 insulin precursor [Aplysia californica]
MSKFLLQSHSANACLLTLLLTLASNLDISLANFEHSCNGYMRPHPRGLCGEDLHVIISNLCSSLGGNRRF
LAKYMVKRDTENVNDKLRGILLNKKEAFSYLTKREASGSITCECCFNQCRIFELAQYCRLPDHFFSRISR
TGRSNSGHAQLEDNFS
>AAA40590.1 insulin [Octodon degus]
MAPWMHLLTVLALLALWGPNSVQAYSSQHLCGSNLVEALYMTCGRSGFYRPHDRRELEDLQVEQAELGLE
AGGLQPSALEMILQKRGIVDQCCNNICTFNQLQNYCNVP
>KAB1251309.1 Insulin [Camelus dromedarius]
MALWTRLLALLALLALGAPTPARAFANQHLCGSHLVEALYLVCGERGFFYTPKARREVEDTQVGGVELGG
GPGAGGLQPLGPEGRPQKRGIVEQCCASVCSLYQLENYCN
>NP_001035835.1 insulin, isoform 2 precursor [Homo sapiens]
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQASALSLSS
STSTWPEGLDATARAPPALVVTANIGQAGGSSSRQFRQRALGTSDSPVLFIHCPGAAGTAQGLEYRGRRV
TTELVWEEVDSSPQPQGSESLPAQPPAQPAPQPEPQQAREPSPEVSCCGLWPRRPQRSQN
>NP_571131.1 insulin preproprotein [Danio rerio]
MAVWLQAGALLVLLVVSSVSTNPGTPQHLCGSHLVDALYLVCGPTGFFYNPKRDVEPLLGFLPPKSAQET
EVADFAFKDHAELIRKRGIVEQCCHKPCSIFELQNYCN
>pir||INCD insulin - cod (Gadus sp.)
MAPPQHLCGSHLVDALYLVCGDRGFFYNPKGIVDQCCHRPCDIFDLQNYCN
>pir||INHY insulin - hamster
FVNQHLCGSHLVEALYLVCGERGFFYTPKSGIVDQCCTSICSLYQLENYCN
>AAB60625.1 insulin [Ovis aries]
MALWTRLVPLLALLALWAPAPAHAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVEGPQVGALELAG
GPGAGGLEGPPQKRGIVEQCCAGVCSLYQLENYCN
>XP_014388588.1 PREDICTED: insulin [Myotis brandtii]
MALWTRLLPLLALLALWAPTPAQAFYFEHLCDEDLAEMLTIICGDQGFRNPKATRELPDPQEGEVDMGAG
GQKALTLEQLLQNSDIPARLLALWAPAPAPAQSGEQRLCGEDLVDTLTMVCGDRGFYSPTALRELPDPQE
GEVDMGAGGQKALTLEQLLQNSDIVDMCCNNFCSFYQLEYYCN
>AAA19033.1 insulin [Oryctolagus cuniculus]
MASLAALLPLLALLVLCRLDPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKSRREVEELQVGQAELGG
GPGAGGLQPSALELALQKRGIVEQCCTSICSLYQLENYCN
>pir||INMKSQ insulin - common squirrel monkey
FVNQHLCGPHLVEALYLVCGERGFFYAPKTGVVDQCCTSICSLYQLQNYCN
>pir||INOS insulin - ostrich
AANQHLCGSHLVEALYLVCGERGFFYSPKAGIVEQCCHNTCSLYQLENYCN
>pir||INEL insulin - elephant
FVNQHLCGSHLVEALYLVCGERGFFYTPKTGIVEQCCTGVCSLYQLENYCN
>AAF80383.1 insulin precursor [Aplysia californica]
MSKFLLQSHSANACLLTLLLTLASNLDISLANFEHSCNGYMRPHPRGLCGEDLHVIISNLCSSLGGNRRF
LAKYMVKRDTENVNDKLRGILLNKKEAFSYLTKREASGSITCECCFNQCRIFELAQYCRLPDHFFSRISR
TGRSNSGHAQLEDNFS
>pir||INTK insulin - turkey (tentative sequence)
AANQHLCGSHLVEALYLVCGERGFFYSPKAGIVEQCCHNTCSLYQLENYCN
>AAA59172.1 insulin [Homo sapiens]
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG
GPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
>QBX89050.1 insulin, partial [Nephrops norvegicus]
VVVVVVGSSRASRRTYPTSEEEPRRRLCGWRLANKLNRVCKGVYNNPGSTGNYLFYRSRRDGESEPGLPP
EEYLDLLPDPEEERGLRHHYLTFSQRASEDTPSEENEAPGSFFGSLSPQDSPHQSAVQEDEASSVQFPFL
TEEEASQMVRVRPRSKRGLSAECCRKVCTVSELVGYCY
>ACQ91106.1 insulin, partial [Haliotis corrugata]
DLHVIISNLCSSLGGNRRFLAKYMVKRDTENVNDKLRGILLNKKEAFSYLTKREASGSITCECCFNQCRI
FELAQYCRLPDHFFSRISRTG
>BAS32722.1 insulin, partial [Varanus exanthematicus]
LVLLAVLAPTAIYATSENDEHLCGSALVEALVSACGKEGIYSFTKRNEQSLGHGLLDNEVPFHLGKRGIV
EDCCENICPWSVLQSYCR
>ELK28555.1 Insulin [Myotis davidii]
MALWTRLLPLLALLALWAPAPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKDRRELPDPQGESSPLTP
RSHPKGTGYLASVDPSQSQDQHLCGDELVNALTITCGDRGFYNPMAPLEQDDLQEEEVEMDEGGLQALTL
EGLLQKRGIVEECCTNVCSLYQLERYCN</pre>
<h3 style="color: green; padding-bottom: 10px;">Brief Video Tutorial</h3>
<p><iframe width="560" height="315" src="https://www.youtube.com/embed/_T07AAMcK8A" frameborder="0" allowfullscreen></iframe></p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com1tag:blogger.com,1999:blog-1315445647083902393.post-74607175763209066562020-11-14T18:14:00.005+05:302020-11-16T07:43:12.348+05:30Synthesis and Retrosynthesis of Molecule(s) for Drug Development using IBM RXN<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<p><a href="https://drive.google.com/uc?export=view&id=115kpz79f3pw1xkaVO5WXk7-PMtedzEfV" target="_blank"><img alt="IBM RXN" src="https://drive.google.com/uc?export=view&id=115kpz79f3pw1xkaVO5WXk7-PMtedzEfV" style="display: block; margin: 0 auto; padding-bottom: 20px;" /></a></p>
<p>Synthesis is a step-by-step process of constructing complex molecules using a set of molecules and specific reagents. While retrosynthesis (retro- backwards) is the process of deconstructing a molecule into readily available simple molecules. IBM RXN is the first, FREE artificial intelligence (AI) web service for predicting reactions and retrosynthesis molecules. Moreover, the AI model is independent of atom-mapping and give back a confidence level of the prediction. In this tutorial, I have explained synthesis and retrosynthesis of a molecule using IBM RXN. List of resources used in this video tutorial are <a href="https://rxn.res.ibm.com/" target="_blank">IBM RXN</a>, and <a href="https://pubchem.ncbi.nlm.nih.gov/" target="_blank">NCBI PubChem</a>.</p>
<p style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="270" width="480" src="https://www.youtube.com/embed/rWAZDZ56cj8"></iframe>
</p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-5253100461404101122020-10-12T12:27:00.002+05:302021-02-11T21:13:21.822+05:302D Plot and 3D Visualization of Protein-Ligand and Protein-Protein Interactions<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<p><a href="https://drive.google.com/uc?export=view&id=1KVobfYzS-KmyqttNLBOejqOqOUb2vW5I" target="_blank"><img alt="LigPlus" src="https://drive.google.com/uc?export=view&id=1KVobfYzS-KmyqttNLBOejqOqOUb2vW5I" style="display: block; margin: 0 auto; padding-bottom: 20px;" /></a></p>
<p>Intermolecular interactions are weak bonds formed due to electron sharing between two or more atoms to hold a molecule together. In molecular modelling or computer-aided drug designing (CADD), intermolecular interaction studies are performed to analyze the stability/energy of docking molecules. This video tutorial demonstrates two-dimensional (2D) plot and three-dimensional (3D) molecular visualization of protein-ligand and protein-protein inter-molecular interactions using LigPlot<sup>+</sup>/LigPlus tool. LigPlot<sup>+</sup> is a successor of original LigPlot program. The protein-ligand inter-molecular interactions are computed using LigPlot program and protein-protein or domain-domain inter-molecular interactions using DimPlot program. Moreover, the interactive 3D molecular visualization of the computed result can be viewed using RasMol or PyMOL. List of softwares used in this tutorial are <a href="https://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/" target="_blank">LigPlot<sup>+</sup></a>, <a href="https://www.ebi.ac.uk/thornton-srv/software/LigPlus/" target="_blank">LigPlus</a>, <a href="http://www.openrasmol.org/" target="_blank">RasMol</a>, <a href="https://pymol.org/2/" target="_blank">PyMOL</a>, and <a href="https://www.oracle.com/in/java/technologies/javase/javase-jdk8-downloads.html" target="_blank">JDK</a>.</p>
<p style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="270" width="480" src="https://www.youtube.com/embed/9GPStZ1T4Zg"></iframe>
</p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-81049594787491091332020-10-09T11:29:00.001+05:302020-10-27T09:17:10.738+05:30Splitting PDB File into Chains and Ligands Without using Tools<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<p><a href="https://drive.google.com/uc?export=view&id=1yPIxs2rcCr18UJaFBlm0d-RVFIww_T6s" target="_blank"><img alt="SPLIT PDB File" src="https://drive.google.com/uc?export=view&id=1yPIxs2rcCr18UJaFBlm0d-RVFIww_T6s" style="display: block; margin: 0 auto; padding-bottom: 20px;" /></a></p>
<p>Protein Data Bank (PDB) file format is a representation of a three-dimensional (3D) structure of the protein and ligand data extracted by interpreting the experimental result of high-energy electromagnetic radiation (X-ray) or Nuclear Magnetic Resonance (NMR) through the computational method. The standard <a href="http://www.wwpdb.org/documentation/file-format.php" target="_blank">PDB file format</a> was created by RCSB during the 1970s for parsing through software.</p>
<p>The atomic coordinate entries of protein are represented by <b>ATOM</b> & <b>TER</b> fields, and ligand by <b>HETATM</b> field (given in the table below).</p>
<p>
<table border="1" cellspacing="0" cellpadding="3" style="width: 100%; text-align: center; vertical-align: middle; border-collapse: collapse; border: 1px solid blue">
<tbody style="text-align: left">
<tr style="text-align: center"><th>Record Type</th><th>Columns</th><th>Description</th></tr>
<tr><td rowspan="16" valign="top">ATOM</td><td>1 - 4</td><td>"ATOM"</td></tr>
<tr><td>7 - 11</td><td>Atom serial number</td></tr>
<tr><td>13 - 16</td><td>Atom name</td></tr>
<tr><td>17</td><td>Alternate location indicator</td></tr>
<tr><td>18 - 20</td><td>Residue name</td></tr>
<tr><td>22</td><td>Chain identifier</td></tr>
<tr><td>23 - 26</td><td>Residue sequence number</td></tr>
<tr><td>27</td><td>Code for insertions of residues</td></tr>
<tr><td>31 - 38</td><td>X orthogonal Å coordinate</td></tr>
<tr><td>39 - 46</td><td>Y orthogonal Å coordinate</td></tr>
<tr><td>47 - 54</td><td>Z orthogonal Å coordinate</td></tr>
<tr><td>55 - 60</td><td>Occupancy</td></tr>
<tr><td>61 - 66</td><td>Temperature factor</td></tr>
<tr><td>73 - 76</td><td>Segment identifier</td></tr>
<tr><td>77 - 78</td><td>Element symbol</td></tr>
<tr><td>79 - 80</td><td>Charge</td></tr>
<tr><td rowspan="2" valign="top">HETATM</td><td>1 - 6</td><td>"HETATM"</td></tr>
<tr><td>7 - 80</td><td>same as ATOM records</td></tr>
<tr><td rowspan="6" valign="top">TER</td><td>1 - 3</td><td>"TER"</td></tr>
<tr><td>7 - 11</td><td>Serial number</td></tr>
<tr><td>18 - 20</td><td>Residue name</td></tr>
<tr><td>22</td><td>Chain identifier</td></tr>
<tr><td>23 - 26</td><td>Residue sequence number</td></tr>
<tr><td>27</td><td>Code for insertions of residues</td></tr>
</tbody>
</table>
</p>
<p>Separation of PDB files to chains and ligands are most important in comparative/homology/molecular modelling and Computer-aided Drug Design. In this tutorial, a text editor is used to separate the PDB file into chains and ligands. The resource and software used in this video tutorial are <a href="https://www.rcsb.org/" target="_blank">RCSB PDB</a> and <a href="https://notepad-plus-plus.org/" target="_blank">Notepad++</a>.</p>
<p style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="270" width="480" src="https://www.youtube.com/embed/TjtVh22w13A"></iframe>
</p>
<p><b>Note:</b> The text editor must be an ASCII character only supported editor (not rich text editor). Moreover, the file name extension should end with <b>.pdb</b>.</p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-34403589981642440222020-09-19T12:07:00.001+05:302020-09-19T12:07:47.981+05:30Prediction of 3D Structure (Folding) of a RNA Sequence<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<p><a href="https://drive.google.com/uc?export=view&id=1YtwL8SBaFNQi_gksAZXrZtyDftr4jOFg" target="_blank"><img alt="RNA Structure" src="https://drive.google.com/uc?export=view&id=1YtwL8SBaFNQi_gksAZXrZtyDftr4jOFg" style="display: block; margin: 0px auto; padding-bottom: 5px;" /></a></p>
<p>Ribonucleic acid (RNA) is a linear single-stranded molecule that takes part in translation to protein. The intramolecular interactions (<i>a.k.a.</i> folding) of RNA base pairs (A=U and C≡G) form a secondary structure. Nussinov (or) Zuker algorithm is a dynamic programming approach used for the prediction of the secondary structure of the RNA. The dot-bracket structure with the minimum free energy is a stable secondary structure.</p>
<p>Prediction of the three-dimensional (3D) structure of RNA using mFold and RNAComposer tools have demonstrated in this tutorial. The mFold tool predicts the dot-bracket notation format RNA folding result from the RNA sequence, while the RNAComposer tool predicts the 3D structure from the dot-bracket notation. The resources used in this tutorial are <a href="https://www.ncbi.nlm.nih.gov/" target="_blank">NCBI GenBank</a>, <a href="http://unafold.rna.albany.edu/?q=mfold" target="_blank">mFold</a>, and <a href="http://rnacomposer.cs.put.poznan.pl/" target="_blank">RNAComposer</a>.</p>
<p style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="270" src="https://www.youtube.com/embed/YB13BkjN8RA" width="480"></iframe>
</p>
<p><b>Note:</b> The length of RNA sequence input in <b>mFold</b> is limited to 4000 bases and sequence/dot-bracket notation input in <b>RNAComposer</b> is limited to 500 bases, due to the complexity of the algorithm used in the programs.</p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0tag:blogger.com,1999:blog-1315445647083902393.post-58311666302853904402020-09-13T22:00:00.001+05:302020-10-27T09:18:00.704+05:30Constructing Entropy Plot from Multiple Sequence Alignment<div style="color: black; font-family: 'times new roman', serif; font-size: 12pt; text-align: justify;">
<p><a href="https://drive.google.com/uc?export=view&id=1Bkqm7sjixhzIWuAZkbVg8qZOY--r4XwK" target="_blank"><img alt="Entropy Plot" src="https://drive.google.com/uc?export=view&id=1Bkqm7sjixhzIWuAZkbVg8qZOY--r4XwK" style="display: block; margin: 0px auto; padding-bottom: 5px;" /></a></p>
<p>The entropy in sequence analysis refers to the measure of the variation of characters (column) in multiple sequences. Entropy plot through multiple sequence alignment can be predicted using different types of entropy formulas, namely <i>Shannon's Entropy</i>, <i>Schneider's Entropy</i>, <i>Shenkin's Entropy</i>, <i>Gerstein's Entropy</i>, and <i>Gap normalized Entropy</i>.</p>
<p>Prediction of entropy plot consists of two phases: (<i>i</i>) performing multiple sequence alignment and consensus, and (<i>ii</i>) calculation of entropy number for each column through consensus of multiple sequence alignment. The entropy plot is generated by plotting vertical lines in the order of the consensus sequence on the <i>x</i>-axis, and the entropy number on the <i>y</i>-axis. This simple video tutorial demonstrates how to predict entropy plot through multiple sequence alignment. The tools used in this tutorial are <a href="https://www.genome.jp/tools-bin/clustalw" target="_blank">ClustalW</a>, and <a href="https://www.hiv.lanl.gov/content/sequence/ENTROPY/entropy_one.html" target="_blank">Entropy Plotter</a>.</p>
<p style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="270" src="https://www.youtube.com/embed/00QQQcuvDCM" width="480"></iframe>
</p>
<p><b>Note:</b> We can choose any multiple sequence alignment tool, but the alignment output must be FASTA file format.</p>
</div>Prof. Dr. T. Ashok Kumarhttp://www.blogger.com/profile/14677658375016995194noreply@blogger.com0