BioGem Blog

loc BLAST is a PHP library that provides a graphical user interface (GUI) for the command-line NCBI BLAST+ programs. The official Docker image of loc BLAST is available on Docker Hub . 💿 Using NCBI Docker Images for Web BLAST The most straightforward way to run a web-based BLAST service with Docker is to use a pre-built image provided by the NCBI: NCBI BLAST+ Command Line Tools: The NCBI provides official Docker images for the standalone command-line BLAST+ suite, which can be found on their GitHub page and Docker Hub . Latest version: The ncbi/blast:latest tag generally points to the most recent stable release. Specific versions: You can specify a particular version, e.g., ncbi/blast:2.14.1 , to ensure reproducibility. 🛠️ Setting up loc BLAST in a Docker Environment To use loc BLAST , you would need to deploy it within a web server environment that also has access to the NCBI BLAST+ binaries. loc BLAST requires a web serv...

The AlphaFold Server is a free, web-based platform launched by Google DeepMind and Isomorphic Labs to provide the scientific community with access to AlphaFold 3 . While the original AlphaFold was revolutionary for predicting protein structures, the AlphaFold 3 server expands this capability to virtually all “life’s molecules,” allowing researchers to model how proteins interact with DNA, RNA, ligands, and more in a single, unified system. 🧬 Key Capabilities Unlike its predecessors, the AlphaFold 3 server is a multimodal model. It doesn't just fold proteins; it predicts the joint 3D structure of complex molecular assemblies. Protein-Ligand Interactions: Accurately models how small molecules (drugs) bind to proteins, showing a 50% improvement over traditional docking methods. Nucleic Acids: Predicts the structures of DNA and RNA and how they interact with proteins (e.g., transcription factors or CRISPR complexes). Chemical Modifications: Pr...

A step-by-step Bioinformatics protocol for Next-Generation Sequencing (NGS) are, Data quality control using tools like FastQC to assess raw data. Data preprocessing for adapter trimming and low-quality base removal with tools like Trimmomatic or FastP. Read mapping to a reference genome using aligners such as BWA or Bowtie2. Post-alignment processing including duplicate removal with Picard and variant calling with GATK or Samtools. Downstream analysis and visualization for specific applications like differential gene expression or variant interpretation using tools like R packages or IGV. A more detailed breakdown of those were given below 1. Data Quality Control (QC) Purpose: To check the quality of the raw sequencing reads and identify any potential issues. Tools: FastQC: A widely used tool to generate quality control reports for raw sequencing data. Output: A report summarizing metrics like Phred scores, adapter contamination, and sequence qu...

A simple Gnuplot script designed to generate a customized 2D line plot of potential energy data (presumably vs. simulation steps or time), using data from a file named PE.txt (available in GitHub ). The script applies several visual formatting settings to make the plot visually appealing and informative. This script produces a clean, stylized 2D plot of potential energy vs. simulation steps with (1) custom fonts, colors, and line styles, (2) no legend, (3) margins around the x-axis, and (4) automatic y-axis scaling. Source Code set title '{/Times-New-Roman=14:Bold Potential Energy Plot}' tc rgb '#167116' set xlabel '{/Arial:Italic Number of steps}' tc rgb 'red' set ylabel '{/Arial:Italic Potential energy}' tc rgb 'red' set style line 1 lt 1 lc rgb '#f70453' lw 0.5 set grid layerdefault lt 0 lc rgb 'blue' lw 0.5 set border lt 1 lc rgb 'blue' lw 1 unset key plot 'PE.txt' with lines ls 1 set xrang...

Performing a Molecular Dynamics (MD) simulation of a small molecule in UCSF Chimera involves a series of steps to prepare the molecule, set up the simulation environment, run the simulation, and finally, analyze the resulting trajectory. Here's a step-by-step guide for the same: 1. Loading and Preparing the Small Molecule Structure Open Chimera: Launch UCSF Chimera or ChimeraX. Load your molecule: Import your small molecule structure into Chimera using File > Open or File > Fetch by ID if the structure is available in a database like the Protein Data Bank (PDB). Add Hydrogens: Use the "Molecular Dynamics Simulation" tool's "Prep Structure" section to add hydrogens. You might also be able to use the addh command. Assign Force Field Parameters: Since you are working with a small molecule (a nonstandard residue), you will use Amber's Antechamber module, which is included in Chimera, to assign force field parameters. This involves ass...

UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a distance-based method for constructing phylogenetic trees. It works by iteratively clustering the two closest groups of sequences together, forming a new cluster until all sequences are grouped into a single tree. The distances between clusters are calculated using the average of all pairwise distances between sequences within those clusters. UPGMA produces rooted trees, meaning it has a defined root representing the common ancestor. Here's a more detailed explanation: 1. Distance Matrix UPGMA begins with a distance matrix, which contains the pairwise distances between all sequences being compared. These distances can be based on sequence alignment, protein structure comparisons, or other relevant metrics. \[D_{i,j}=\max\begin{cases}D_{i-1,j-1} & + & s(a_i,b_j) \\D_{i-1,j} & + & s(a_i,-) \\D_{i,j-1} & + & s(-,b_j)\end{cases}=\max\begin{cases}D_{i-1,j-1}& + ...

Prediction of functional regions in the protein sequence plays a crucial role in the computer-aided drug discovery. SMART (a Simple Modular Architecture Research Tool) helps identify and annotate protein domains and analyze domain architectures by BLAST search. In bioinformatics, domains refer to distinct functional, structural, or evolutionary units within proteins, DNA, or RNA. Here are some key types of domains in bioinformatics: 1. Protein Domains Structural Domains : Compact, independently folding units within a protein (e.g., SH3, zinc finger, immunoglobulin domains). Functional Domains : Regions responsible for specific biochemical activities (e.g., kinase domain, DNA-binding domain). Evolutionary Domains : Conserved regions indicating common ancestry (e.g., Pfam domains). 2. DNA/RNA Domains Regulatory Domains : DNA regions controlling gene expression (e.g., promoters, enhancers). Functional RNA Domains : Motifs in non-coding RNAs (e.g., ribozyme catalytic cor...

This page is designed to extract the video ID from a YouTube video URL. I have used a simple JavaScript regular expression to match the pattern and extract the video ID from the string. The JavaScript regular expression code is provided below, /[?=/]([A-Za-z0-9_-]{10}[AEIMQUYcgkosw048])[?=/]*?/g Live demonstration: YouTube Video ID Grabber Enter the YouTube URL Regular Expression Explanation [ Character set. Match any character in the set. ? Character. Matches a "?" character (char code 63). = Character. Matches a "=" character (char code 61). / Character. Matches a "/" character (char code 47). ] ( Capturing group #1. Groups multiple tokens together and creates a capture grou...

Google has released an amazing animation effect that appears when you click on the apple on the page that appears when you search for " Isaac Newton " or " Sakura ." This is my simple try with a tiny JavaScript to create additional effects, like more apples falling automatically without clicking on the apple image. The effect appears on the screen as a live wallpaper. The JavaScript code used in the video tutorial is bellow, setInterval(function() { document.getElementsByClassName("smm4bb")[0].click(); }, 100); Note: To paste code into the terminal, enter "allow pasting" when requested. If you don't put "allow pasting," nothing will happen and no code will be pasted. The warning won't appear again after pasting permission has been granted.

Orion refers to a prominent constellation ( a group of fixed stars ) visible to the naked eye. It is named after a hunter in Greek mythology and is easily recognizable due to its distinctive shape and bright stars, such as Betelgeuse and Rigel . Whereas Orion's Belt is a pattern in the constellation of Orion. This belt consists of three bright stars— Alnitak , Alnilam , and Mintaka —aligned in a straight line, making it one of the most identifiable features in the night sky. Many cultures have their own interpretations of Orion's Belt, often associating them with various myths and legends. In this article, the Orion's Belt is connected to a Hindu mythology. Sanskrit Tamil Name Star Name Constellation Position Uṣā உஷா Alnitak Zeta (ζ) Orion 0°49’ Aniruddha அனிருத்தா Alnilam Epsilon (ε) Orion 29°36’ Citralekhā சித்ரலேகா Mintaka Delta (δ) Orion 28°30’ The Orion's Belt is seen in the image above, which is associated with Greek mythology. T...

NTSYSpc (Numerical Taxonomy and Multivariate Analysis System) is a simple and light-weight statistical software used for cluster analysis of molecular genetic qualitative data. The broad features of NTSYSpc include similarity/dissimilarity, clustering, graph theoretic methods, ordination, interactive graphics, multivariate tests, geometric morphometrics, and comparison of matrices. This brief video tutorial illustrates how to use NTSYSpc to create a cladogram ( a tree diagram that shows the cladistic relationship between several populations/species ) from a binary matrix. The table made up of 0s and 1s is represented by the binary matrix. On the other hand, 1 denotes the presence of character, 0 denotes the absence of character ( trait ), and a blank area denotes the absence of character.

It is an online free mathematics problem solving tool by Google. Your maths problem will be shared with maths providers ( GeoGebra, QuickMath, Alpertron, Mathway, Symbolab, eMathHelp, Tiger Algebra, Gauthmath, Matrix Calculator, dCode, TutorEva, MathCelebrity, Qanda, CameraMath, ScanMath, Mathforyou, or MathDF ) and processed according to their privacy policies. No other data will be shared. It supports both manual problem typing and scan and upload images (process through OCR technology). We can solve a variety of problems namely linear equations, polynomials, quadratic equations, rational expressions, exponents, complex numbers, trigonometry, inequalities, system of linear equations, radicals, absolute values, logarithms, probably, integrals, derivatives, vectors, and matrices . The rich feature of the tools is that we can get a step-by-step explanation of the problem solving.

Homology or comparative protein structure modeling is a complex process, but with the help of tools like Modeller , it becomes more accessible and efficient. It's fascinating how the program can automatically calculate a model with all non-hydrogen atoms based on an alignment of a sequence to be modeled with known related structures. The input to Modeller are restraints on the spatial structure of the amino acid sequence(s) and ligands to be modeled, and the output is a 3D structure that satisfies these restraints as well as possible. It's amazing how the program can derive restraints from various sources such as related protein structures, NMR experiments, rules of secondary structure packing, cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, residue-residue and atom-atom potentials of mean force, and even intuition. The program can operate on various spatial features defined by atoms or pseudo at...

BioEdit 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. The BioEdit software provides automated local and web BLAST ( B asic L ocal A lignment S earch T 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 BioEdit software to support NCBI BLAST . The tutorial also covers how to perform a query search, specifically pairwise sequence alignment, against the database.

A phylogenetic tree ( a.k.a. , 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 i nteractive T ree O f L ife ( iTOL ) 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. This is a simple video tutorial for user interactive visualization of phylogenetic trees using the iTOL tool. The iTOL 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.

A phylogenetic tree ( a.k.a. , 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. This is a simple video tutorial for constructing a phylogenetic tree using Molecular Evolutionary Genetics Analysis ( MEGA ) software. The MEGA software produces phylogenetic trees from multiple sequences in various formats: rectangular, slanting, curved, radial, and curved.

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. 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, Tuppe...

JME/JSME is a free and open-source molecule editor developed by Peter Ertl and Bruno Bienfait. JSME (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. Jmol/JSmol is a free and open-source molecule visualization tool developed by Bob Hanson . JSmol (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. JSmol in collaboration with JSME, has implemented a 2D ( SMILES string) to 3D structure conversion method by integrating the API of the CACTUS server. The link to an interactive demo of JSME and JSmol is here . B...