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Prediction of 3D Structure (Folding) of a RNA Sequence

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Ribonucleic acid (RNA) is a linear single-stranded molecule that takes part in translation to protein. The intramolecular interactions (a.k.a. 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.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 NCBI GenBank, mFold, and RNAComposer.Note: The length of RNA sequence input in mFold is limited to 4000 bases and sequence/dot-bracket notation input in RNAComposer is limited to 500 bases, due to the complexity of the algo…

Multiple Sequence Alignment and Entropy Plot

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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 Shannon's Entropy, Schneider's Entropy, Shenkin's Entropy, Gerstein's Entropy, and Gap normalized Entropy.Prediction of entropy plot consists of two phases: (i) performing multiple sequence alignment and consensus, and (ii) 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 x-axis, and the entropy number on the y-axis. This simple video tutorial demonstrates how to predict entropy plot through multiple sequence alignment. The tools used in this tutorial are ClustalW, and Entropy Plotter.Note: We can choose any multiple sequence alignment tool, but the alignment output must be FASTA file format.

Chemical Name to 3D Structure Prediction

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The three-dimensional (3D) structure of a compound can be retrieved using standard chemical nomenclature from the most popular databases, namely PubChem, ChEBI, ChEMBL, ChemSpider, CSD, ZINC, DrugBank, etc. If the 3D structure or chemical data is not available in the database, this simple tutorial helps you to predict the most optimal structure. The tools used in this tutorial are OPSIN, CACTUS, and Chimera.

Epidemiology and Gene Diversity of COVID-19 through NextStrain

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain of coronavirus that causes coronavirus disease 2019 (COVID-19). The epidemiology study of COVID-19 reveals the incidence, distribution, and control of disease in different groups of people over regions. This tutorial helps you to find the current gene diversity of SARS-CoV-2 through epidemiology study.

Finding Current Gene Diversity of SARS-CoV-2 through NCBI

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain of coronavirus that causes coronavirus disease 2019 (COVID-19). It causes gene mutation in itself and the host organism, through receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2) complex. The mutation level increase when it transmitted to other organisms. Gene diversity of the SARS-CoV-2 can found by constructing a phylogenetic tree through multiple sequence alignment of genome sequences. This tutorial helps you to find the current gene diversity of SARS-CoV-2.

Molecular Graphics Models using Swiss PDB Viewer

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This tutorial presents various models of molecular graphics representations such as Wireframe model, Ball & Stick model, Spacefill model, Surface model, Stick model, Backbone model, Van der Waals model, Ribbon model, Strand model, and Electrostatic potential model of protein structure using Swiss PDB Viewer.ProtocolOpen Swiss PDB Viewer software.Click FileOpen PDB File… menu to browse protein structure (.pdb file) location. By default, it displays protein structure in “Wireframe” model.In Control Panel window, right-click symbol “::v” to display whole protein structure in “Van der Waals” model.Click DisplayRender in Solid 3D menu, and click DisplayShow Backbone Oxygens menu (deselect) to display protein structure in “Sticks” model.In Control Panel window, right-click symbol “side” to display whole protein structure in “Backbone” model.In Control Panel window, right-click symbol “ribn” and “show” to display whole protein structure in “Ribbons in Cartoons” model.Click Color act …

Bouncing Text Animation Effect using Pure CSS

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This is a simple tutorial for creating bouncing text animation effect using pure CSS3 and HTML. In this tutorial, I have used CSS3 animation property with value ease to move text (keyframe) towards top and bottom (alternate -- distance -10px) at 1 second rate infinitely (infinite).Source CodeHTML: index.html<!DOCTYPE html> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <title>Bouncing Text Animation Effect</title> <link href="style.css" rel="stylesheet" type="text/css" /> </head> <body> <div id="title_wrapper"> <div id="text"> <i>B</i><i>o</i><i>u</i><i>n</i><i>c</i><i>i</i><i>n</i><i>g</i><i></i> <i>T</i><i>e</i><i>x</i><i>t</i><i>…