Collection of scripts written in Perl or Python for some everyday as well as specific Bioinformatics tasks.

count.pl : Counts the number of sequences in a multiple FASTA file.
Usage : count.pl <file.fasta>

filter_duplicate.pl : Filters duplicate sequences in a multiple FASTA file.
Usage : filter_duplicate.pl <file.fasta>
Note : Depends on BioPerl

length.pl : Calculates length of sequence(s) in FASTA format.
Usage : length.pl <file.fasta>

blastxml_query_coverage.pl : Parse BLAST XML output (downloaded from the NCBI BLAST website), to fetch sequences with a desired query coverage (percentage).
Usage : blastxml_query_coverage.pl <file.xml> <query-coverage %>
Note : Depends on XML::Simple

extractdomains_refseq.pl : Reads hmmsearch output from HMMER software and extracts matched sequences in FASTA format.
Usage : extractdomains_refseq.pl
Note : hmmsearch must be done against refseq database.

extractdomains_trembl.pl : Reads hmmsearch output from HMMER software and extracts matched sequences in FASTA format.
Usage : extractdomains_trembl.pl
Note : hmmsearch must be done against trembl database.

atom2hetatm.pl : Converts the ATOM flag to HETATM flag for the ligand residue in the HADDOCK output file.
Usage : atom2hetatm.pl <file.pdb>

rmsd_matt.pl : Calculates the RMSD between a reference structure and a structure extracted from a file containing multiple PDB (generated using VMD).
Usage : rmsd_matt.pl <reference-structure.pdb> <multi.pdb>