MEME suite is used to discover novel motifs in unaligned nucleotide and protein sequences [1,2]. In this article, we will learn how to install MEME on...
EasyVS is a web-based bioinformatics tool that simplifies the selection of the molecular library and its virtual screening [1]. Users can easily perform virtual screening of...
BLAT is a pairwise sequence alignment algorithm that is used in the assembly and annotation of the human genome [1]. In this article, we will install...
It is a challenging task to discover somatic coding indels that are generated during the preparation of the PCR-based RNA-seq library. A new tool called RNAIndel [1]...
Differential gene expression analysis helps in discovering quantitative changes in the expression levels between the experimental groups. For that, statistical testing is done using various software....
CRISPR/Cas9 is a genome editing technology trending fastly. It is used to identify CRISPR associated genes within the genomes of prokaryotic bacterias. Several tools are available...
We have provided several tutorials on Autodock Vina software [1] including its installation on Ubuntu. This article is a guide to installing Autodock Vina on Windows...
It is computationally costly to predict target proteins for query compounds or a chemical library to be run on a local computer. A new tool called...
Openbabel is used to inter-convert many file formats [1]. It is available for Linux, Windows, and MAC operating systems. In this article, we will learn how...
Gene expression in single cells is measured using single-cell RNA sequencing technology. It helps in finding new and available cell types of different tissues and organs....
CASTp (Computed Atlas of Surface Topography of proteins) server is used to predict binding pockets and cavities in proteins [1]. It displays binding pockets precisely and...
Docking software such as Autodock4 [1] and Autodock Vina [2] require input receptor and ligand files in a specific format called pdbqt. Sometimes, preparing files using Autodock...
Variant Call Format (VCF) is a text file format used to store thousands of genomic datasets. Since these files consist of a large number of gene...
CHARMM (Chemistry at Harvard Molecular Mechanics) is a molecular simulation program that can be used for simulation of macromolecules, complexes, and many-particle systems [1]. In this...
SALI MODELLER [1] is one of the most widely used command-line bioinformatics software for protein structure prediction based on homology modeling. The installation of MODELLER on...
PyMol is a molecular visualization software that is freely available for education-use-only [1]. PyMol provides an interface for the visualization of small and macromolecules. Besides, it...
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...
Clustal Omega [1,2] and MUSCLE are bioinformatics tools that are used for multiple sequence alignment (MSA). In one of our previous articles, we explained the usage...
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 has become an important methodology in research covering systems consisting of millions of atoms. We have provided several articles on MD simulation...
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