In the last article on Bioinformatics Review, the utilization of Roary [1] and Prokka [2] was explained to create a pangenome from isolated genome sequences. This...
Roary is a pangenome genome pipeline, which calculates pangenome of a set of related prokaryotic isolates [1]. It takes annotated assemblies in the gff3 format generated...
Structure modeling of chemical compounds finds essential application in the field of cheminformatics. It is used to study the structural stability, metal-ion bonding, the presence of...
Stem cells are cells that can be differentiated into other types and are thus pluripotent with the ability to become cells of all lineages. Cells found...
Bioinformatics analyses have become long and difficult as it involves a large number of steps implemented for data processing. Bioinformatics pipelines are developed to make this...
Sequence and structural data in bioinformatics are ever-increasing and the need for its analysis is ever-demanding likewise. As bioinformaticians analyze the data with their keen knowledge...
Micro RNAs (miRNAs) are the short endogenous RNAs (~22 nucleotides) and originate from the non-coding RNAs [1], produced in single-celled eukaryotes, viruses, plants, and animals [2]....
This is a video added to our existing tutorial
Most of the times, it is a very tedious job to convert file formats in bioinformatics, especially when we are dealing with phylogeny. Most of the...
The roots of the molecular simulation application can be traced back to physics where it was applied to simplified hard-sphere systems [1]. This field of molecular...
In our previous article, we discussed different multiple sequence alignment (MSA) benchmarks to compare and assess the available MSA programs. However, since the last decade, several...
Multiple sequence alignment (MSA) is a very crucial step in most of the molecular analyses and evolutionary studies. Many MSA programs have been developed so far...
I-Tasser stands for the iterative threading assembly refinement is a well-known tool for ab-initio structure modeling of proteins [1]. It uses secondary-structure enhanced profile-profile threading alignment...
Intrinsically unstructured proteins (IUPs) are the natively unfolded proteins which must be unfolded or disordered in order to perform their functions. They are commonly referred to...
Single nucleotide variation is a change in a single nucleotide in a sequence irrespective of the frequency of the variation. Single nucleotide variants (SNVs) play a very...
AutoDock Vina is one of the most popular software in Bioinformatics, known for molecular docking simulations. I have already explained the docking procedure in my previous...
Sequence alignment is customary to not only find similar regions among a pair of sequences but also to study the structural, functional and evolutionary relationship between...
Enzymes are natural biocatalysts and an attractive alternative to chemicals providing improved efficiency for biochemical reactions. They are widely utilized in industrial biotechnology and biocatalysis to...
Lipids are the essential metabolites in human body performing different functions such as energy storage, endocrine actions, cell signaling, morphogenesis, and so on. Using a lipidomics...
A lot of protein structures are determined on a large scale and submitted in Protein Data Bank (PDB) www.rcsb.org [1]. After the experimental determination of these structures,...
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