We have provided a tutorial on installing GROMACS [1] on Ubuntu with CUDA GPU support. The methods may vary depending upon the requirements of your system....
A new utility is developed to convert variant calling format (VCF) files into HL7 FHIR format for the purpose of genomics electronic health records (EHR) integration....
We have provided several tutorials on docking including both types: blind docking & site-specific docking using Autodock Vina. In this article, we are going to compare...
We use somatic variant callers to detect mutations in cancer samples by comparing sequencing data tumor and normal sample pairs. This is followed by some ad-hoc...
It is necessary to detect highly variable regions in envelopes of viruses as it allows the establishment of the viruses in the human body. A new...
This is a basic tutorial on how to remove the hetero-atoms (HETATMS) and chains from PDB files. It is an important step for computational and molecular...
Clustal packages [1,2] are quite useful in multiple sequence alignments. Especially, when you need specific outputs from the command-line. In this article, we will install CustalW2...
As shown in previous articles, Pymol [1] has several functions. In this article, we will show how to look for disulfide in protein crystal structures using...
Pymol [1] has many functions that you keep finding on exploration. In this article, we will explain how to draw molecules in Pymol.
A new command-line and web tool are developed for easy visualization of pedigree files. These files help to understand the complete family tree in case of...
Computational docking is an important technique in bioinformatics. The docking result interpretation and representation are important as well. There are various software available for docking result...
HMMER tool is used for searching sequence homologs using profile hidden Markov Models (HMMs) [1]. It is also one of the most widely used alignment tools....
Molecular dynamics (MD) simulation is one of the most widely used methods in bioinformatics. It needs high computation time and therefore, performed on workstations and servers....
Cytoscape is a software for the easy visualization of complex networks [1-3]. In this article, we will install Cytoscape on Ubuntu.
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...
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...
Pyrx is a bioinformatics software that is used for virtual screening of a large number of compounds against targets [1]. In this article, we will install...
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