Perl modules

Bioperl

-A collection of perl modules for bioinformatics
-Facilitates sequence retrieval, manipulation, and parsing results of programs like blast, clustalW.
-http://bioperl.org for download and documentation.
-Individual .pm file has info on how to use modules.
-Usually installed: /usr/local/lib/perl5/site_perl/5.8.0/Bio
  1. Bio::Perl, Bio::DB -- access seq databases. Examples: seqret.pl
  2. Bio::Seq -- sequence and its annotation. Examples: seqio.pl
  3. Bio::SeqIO – read sequence from file, and write to file. Example seqio.pl
  4. Bio::Tools:SeqStats -- molecular weight, etc. Example: seqmw.pl
  5. Bio::SearchIO -- parse blast results.


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