Transcriptomic data analysis is an important requirement in biomedical research. The bioinformatics tools available for transcriptomic data analysis provide a user-friendly interface that is easily accessible...
GROMACS [1] is one of the most popular software in bioinformatics for molecular dynamic (MD) studies of macromolecules. We have provided different tutorials regarding MD simulation...
FASTX-toolkit is a command-line bioinformatics software package for the preprocessing of short reads FASTQ/A files [1]. These files contain multiple short-read sequences obtained as an output...
GROMOS96 is a well-known software package used for biomolecular simulations [1]. It can be used for the molecular dynamics simulation of protein, peptide, and protein-ligand complex...
Pyrx is a bioinformatics software that is used for the virtual screening of a large number of compounds against targets [1]. In this article, we will...
MGLTools2 package comes with three different tools for docking: ADFR, AGFR, and AutoSite [1-3]. In this article, we will install this package on Ubuntu.
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...
DIAMOND is a program for high throughput pairwise alignment of DNA reads and protein sequences [1]. It is used for the high-performance analysis of large sequence...
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...
FragGeneScan is a bioinformatics software to find fragmented genes in short reads [1]. It predicts genes by combining sequence models and codon usages in a hidden...
Previously, we have shown how to analyze Vina output of docking in PyMol [1].
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]...
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....
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