AutoSite is a computational method and tool that is used for the identification of binding sites of small molecules in target proteins [1]. It comes with...
A new suite of tools called SequelTools has been developed for analyzing PacBio raw sequence data [1]. Pacbio is a third-generation DNA sequencing method that is...
BCFtools is a set of utilities that are used to manipulate variant call files (VCF) and binary call files (BCF). It can be used for both...
MAIRA is a new software for taxonomic and functional analysis of long reads without requiring any external resource [1]. It can easily facilitate the execution of...
GalaxyPepDock is a software used for protein-peptide docking based on interaction similarity. In this article, we will install GalaxyPepDock on Ubuntu.
In this article, some software/tools are mentioned that are most widely used for RNA secondary structure prediction.
MEGAX is a bioinformatics software/tool used for phylogenetic tree construction. In this article, we will construct a maximum likelihood (ML) tree for a number of protein...
One of the major next-generation sequencing (NGS) technologies that are most frequently used in medical research is Ion Torrent. Software for Ion Torrent machines provides output...
Molecular dynamics (MD) simulation is considered amongst the important methods in bioinformatics. Installation of MD simulation software and execution of their commands is critical. It requires...
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...
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]...
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...
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...
We have published various articles on bioinformatics programming dealing with large files consisting of multiple FASTA sequences. Here is a list of articles related to operations...
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...
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...
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