Protein-protein interactions (PPIs) are essential to study to understand the molecular functions carried out by a group of proteins. Alcala et al., [1] developed a new...
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...
SIFT is a bioinformatics tool for predicting missense effects of non-synonymous/missense variations in sequences [1]. SIFT identifies naturally occurring nonsynonymous polymorphisms as well as laboratory-induced missense...
small open reading frames (smORFs) that are less than 100 codons in length are considered significant. smORFs participate in a variety of biological processes such as...
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...
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...
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...
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...
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....
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