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Bioinformatics Programming

How to concatenate FASTA sequences using Perl?

Dr. Muniba Faiza

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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

sminalog_analysis.py – A new Python script to fetch top binding affinities from SMINA log file

Dr. Muniba Faiza

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sminalog_analysis.py – A new Python script to fetch top binding affinities from SMINA log file

In one of our previous posts, we provided a Python script for the virtual screening analysis of Autodock Vina. This script analyzes all log files obtained from docking of multiple ligands to a receptor and provides the binding affinities for top poses from each file. In this article, we are publishing a new Python script for the virtual screening analysis of SMINA [1]. (more…)

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Bioinformatics Programming

Installing Pycharm on Ubuntu (Linux)

Tariq Abdullah

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Installing pycharm on Ubuntu

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 are going to install Pycharm on Ubuntu. (more…)

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Algorithms

vs_Analysis.py: A Python Script to Analyze Virtual Screening Results of Autodock Vina

Dr. Muniba Faiza

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VS-Analysis: A Python Script to Analyze Virtual Screening Results of Autodock Vina

The output files obtained as a result of virtual screening (VS) using Autodock Vina may be large in number. It is difficult or quite impossible to analyze them manually. Therefore, we are providing a Python script to fetch top results (i.e., compounds showing low binding affinities). (more…)

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