Perl bioinformatics exercises
Perl
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.gitignore
Hydrophobic.pm
LICENSE.txt
README.md
Tmstat.pm
dna_test.pl
pdb_distance.pl
read_fasta.pl
seq_func.pl
test_hydrophobic.pl
translate_fasta.pl

README.md

Perl bioinformatics exercises

Copyright 2011 Lenna X. Peterson arklenna@gmail.com

dna_test.pl attempts to guess whether a sequence is DNA or RNA. It depends on seq_func.pl.

The following files have sample input and output located in data/:

read_fasta.pl reads a multi-record FASTA file and outputs a list of sequence names and lengths.

translate_fasta.pl reads a FASTA file and outputs the 6 possible translations (3 reading frames, forward and reverse complement).

pdb_distance.pl reads a PDB file of a molecule complexed with ADP and outputs a list of every atom within 6 angstroms of the ADP.

test_hydrophobic.pl calls a package that finds the most hydrophobic sequences in a protein. It depends on Hydrophobic.pm and Tmstat.pm.

Another project around the same time used CGI to perform batch BLAST searches of a given sequence against multiple genomes. However, it was a group project so I lack authorization to upload it to github.