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Bioinformatics Programming

Perl script to find duplicate FASTA sequences using their header?

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Perl programming in Bioinformatics

In a large file of FASTA sequences, it is nearly impossible to perform some operations manually.

This is a simple Perl script to find out duplicate sequences in a multi-fasta file using a FASTA header.

Let’s say, your multi-fasta file is ‘sequence.fasta’. 

 

#! /usr/bin/perl
use warnings;
use strict;

my ($infile, $header) = @ARGV;

my $duplicate;
open my $input, '<', $infile or die $!;
while (<$input>) {
    $duplicate = $1 eq $header if /^>(.*)/;
    print if $duplicate;
}

close $input;
exit;

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Bioinformatics Programming

tanimoto_similarities_one_vs_all.py – Python script to calculate Tanimoto Similarities of multiple compounds

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tanimoto_similarities_one_vs_all.py – Python script to calculate Tanimoto Similarities of a compound with multiple compounds

We previously provided a Python script to calculate the Tanimoto similarities of multiple compounds against each other. In this article, we are providing another Python script to calculate the Tanimoto similarities of one compound with multiple compounds. (more…)

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Bioinformatics Programming

tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.

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tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.

RDKit [1] is a very nice cheminformatics software. It allows us to perform a wide range of operations on chemical compounds/ ligands. We have provided a Python script to perform fingerprinting using Tanimoto similarity on multiple compounds using RDKit. (more…)

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Bioinformatics Programming

How to commit changes to GitHub repository using vs code?

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How to commit changes to GitHub repository using vs code?

In this article, we are providing a few commands that are used to commit changes to GitHub repositories using VS code terminal.

(more…)

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