NCBI-BLAST+ [1] command-line tool offers multiple functions to be performed on a large dataset of sequences. Previously, we have shown how to blast against a local...
Dealing with thousands of FASTA sequences is a tedious task without using bioinformatics programming. It eases multiple minute tasks to be performed on FASTA sequences or...
ClustalW2 is a bioinformatics tool for multiple sequence alignment of DNA or protein sequences. It can easily align sequences and generate a phylogenetic tree online (https://www.genome.jp/tools-bin/clustalw)....
Markov Cluster Algorithm (MCL) is a clustering algorithm that clusters networks [1]. One of its applications is in clustering protein or peptide sequences. This is a...
Molecular dynamics (MD) simulation is an important step in studying the dynamics of macromolecules. In one of the previous articles, MD simulation of chain A of...
In our last article, we mentioned the selection pressure analysis of SARS-CoV-2 spike glycoproteins. Now, we have analyzed spike glycoprotein sequences of SARS-CoV. No single purifying...
We have recently conducted a selection pressure analysis on SARS-CoV-2 spike glycoprotein sequences. The analysis revealed not even a single site showing evidence of purifying selection...
A novel coronavirus (CoV), named Severe Acute Respiratory Syndrome-CoV-2 (SARS-CoV-2) or nCoV-2019, has emerged since December 2019 from Wuhan city of Hubei province in China [1]....
Background A journal’s relevance is generally estimated by its impact factor (Web of Science) and the total number of citations of articles published in it. However,...
We have compiled all articles on docking into a Special Issue. This is a complete guide on molecular docking using Autodock Vina for beginners. It includes...
In our last article, we explained the installation of LigPlot+ [1] on Ubuntu. In this article, we will perform protein complex analysis using LigPlot+.
Bioinformatics is rapidly growing since the last few decades and has revolutionized biological research. Researchers are capable of developing therapeutic drugs efficiently, capable of getting rapid...
DeepView (Swiss-PDB Viewer) [1] is used to analyze multiple proteins simultaneously. Protein structure alignment, active site comparison, amino acid mutations, H-bonds, and other relevant functions can...
I have been receiving several e-mails from researchers and students alike regarding the installation of MGL Tools and Autodock Vina on Ubuntu. Most questions are similar in nature,...
PHMMER is a sequence analysis tool used for protein sequences (http://hmmer.org; version 3.1 b2). It is available online as a web server and as well as...
Reading a research article could be a problem for students starting their careers in research. Research papers are sometimes difficult to understand especially when you are...
Molecular docking is the most widely used technique which is used to predict the binding affinities and bound conformations of a ligand and protein complex. Autodock...
Cd-hit is one of the most widely used programs to cluster biological sequences [1]. It helps in removing the redundant sequences and provides better results in...
Multiple sequence alignments (MSAs) are quite valuable in terms of studying new enzymes or organisms. They provide insights to identify their structures and functions. For this...
There are various things which come to mind when someone is going to enter in the field of Bioinformatics and the topmost concern is “Do I...
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