A collection of published articles on different bioinformatics software.

Homology search against a local dataset using NCBI-BLAST+ command-line tool


NCBI-BLAST+ [1] command-line tool offers multiple functions to be performed on a large dataset of sequences. Previously, we have shown how to blast against a local dataset of sequences. This article will explain the search of homologous sequences for a query sequence against a local database of sequences and how to obtain the top 100 hits out of the searched results. Keep Reading

How to use Clustal Omega and MUSCLE command-line tools for multiple sequence alignment?


Clustal Omega [1,2] and MUSCLE are bioinformatics tools that are used for multiple sequence alignment (MSA). In one of our previous articles, we explained the usage of the ClustalW2 command-line tool for MSA and phylogenetic tree construction. In this article, we will use Clustal Omega and MUSCLE for MSA exploring other arguments that facilitate different output formats. Keep Reading

How to perform graph-based clustering of peptide/protein sequences using MCL?


Markov Cluster Algorithm (MCL) is a clustering algorithm that clusters networks [1]. One of its applications is in clustering protein or peptide sequences. This is a fast and scalable clustering algorithm. Previously, we have shown protein/peptide sequence clustering using Cd-hit software. Keep Reading

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