Docking and simulation are two of the methods that are most widely used in bioinformatics. In this article, we provide all important links to the software...
IPD2.0 [1] is an updated version of the Infectious Pathogen Detector (IPD) [2]. It helps in deriving insights from the SARS-CoV-2 genome.
Pycharm [1] is an integrated development environment (IDE) for developers. It combines Python developer tools and provides an easy graphical user interface. In this article, we...
RDP provides analysis tools called RDPTools. These tools are used to high-throughput sequencing data including single-strand, and paired-end reads [1]. In this article, we are going...
cis-regulatory elements are DNA sequence segments that regulate gene expression. cis-regulatory elements consist of some regions such as promoters, enhancers, and so on. These regions consist...
In this article, we are going to install some basic bioinformatics tools on Ubuntu from the repository. These tools include BLAST, HMMER, MUSCLE, MAFFT, several NGS...
Drug-drug interaction is an important method in bioinformatics, especially in the case of treatment of serious diseases such as cancer. It tells us about the drug...
In this article, we summarize the most widely used tools (online/ standalone) for transcription binding site prediction in DNA sequences.
A new bioinformatics tool called “EzMAP” is developed for the easy analysis of the microbiome [1]. EzMAP stands for an easy microbiome analysis platform.
SAMtools is a software package for high-throughput sequencing data analysis [1]. It consists of three separate packages: SAMtools, BCFtools, and HTSlib. We are going to install...
PANDAseq is a bioinformatics tool that aligns paired-ends of Illumina sequences [1]. In this article, we are going to install PANDAseq on Ubuntu.
Visualization of running alignments of reads and contigs facilitates easy analysis and is useful in presenting assembly results. Several tools such as Artemis, BLAST Web, Circos,...
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....
TopHat is one of the most widely used tools for RNA-seq reads to map splice junction [1]. It uses Bowtie to align mammalian genomes. The older...
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....
Bismark is a bioinformatics tool to map bisulfite treated sequencing reads to a genome [1]. It also determines cytosine methylation sites. In this article, we will...
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...
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...
This is a continuation article of our previous post: Tutorial-I: Functional Divergence Analysis using DIVERGE 3.0 software. In our last tutorial, we explained Type-II functional divergence....
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