BioLion has asked for the wisdom of the Perl Monks concerning the following question:

Dear Monks,

A bioinformatics question: I have been doing more and more Gene Ontology (GO) work, specifically, I am looking for enriched terms in my various gene sets. I usually go through the web-based programs like DAVID or Babelomics.

However, I now need a high-throughput approach, but was disappointed to only find GO::TermFinder on CPAN.

There are plenty of GO handlers/parsers available, but far fewer analytical tools, so I wondered if anyone had any experience of doing GO term enrichment on many many groups of genes?

  1. Any particular API I should use?
  2. Any particular problems I should look out for?
  3. Is there another web-based program I should think about?
  4. Is there a downloadable program that might be a good alternate? (i.e. a commandline based one that I can use via perl)
Any help or advice much appreciated!

NB: I have cross-posted a similar question on seqAnswers in an attempt to keep this one BioPerl/perl related...

Just a something something...