Bioinformatics Programming
Perl script to find duplicate FASTA sequences using their header?
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;
Fetching SMILE strings for a given number of SDF files of chemical compounds is not such a trivial task. We can quickly obtain them using RDKit or OpenBabel. But what if you don’t have SDF files of ligands in the first place? All you have is Ligand IDs from PDB. If they are a few then you can think of downloading SDF files manually but still, it seems time-consuming, especially when you have multiple compounds to work with. Therefore, we provide a Python script that will read all Ligand IDs and fetch their SDF files, and will finally convert them into SMILE strings. (more…)
Bioinformatics Programming
How to get secondary structure of multiple PDB files using DSSP in Python?
In this article, we will obtain the secondary structure of multiple PDB files present in a directory using DSSP [1]. You need to have DSSP installed on your system. (more…)
Bioinformatics Programming
vs_analysis_compound.py: Python script to search for binding affinities based on compound names.
Previously, we have provided the vs_analysis.py script to analyze virtual screening (VS) results obtained from Autodock Vina. In this article, we have provided another script to search for binding affinity associated with a compound. (more…)
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