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Bioinformatics Programming

How to concatenate FASTA sequences using Perl?

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Here is a simple Perl script to concatenate multiline FASTA sequences into a single line. A similar Perl script has been provided in one of the previous articles (A Perl script to convert multiline FASTA sequences into a single line). That script is useful for the FASTA files consisting of sequences split into a particular number of residues per line. The script provided in this article can also be used for large files consisting of multiple FASTA sequences split into the indefinite number of residues per line.

Let’s name the multiline FASTA input file as “input.fa”.

#!/usr/bin/perl -w
use strict;

my $input_fasta="input.fa";
open(FILE,"<$input_fasta") || die ("Error opening $input_fasta $!"); 
my $line = ; 
print $line; 
while ($line = ) 
{ chomp $line; 
  if ($line=~m/^>;(.*)/) 
       { print "\n",$line,"\n"; }
  else { print $line; }
}

print "\n";
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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