[Bioperl-l] Newbie Questions: bioperl, bioperl-db, and GO

jjmail at mac.com jjmail at mac.com
Thu Apr 14 00:26:25 EDT 2005

Question 1:

I am brand new to bioperl and the related projects so please forgive my ignorance on this. I have a large list of protein names and I would like to use bioperl to get the corresponding Gene Ontology (GO) information for each protein.

So far I have installed bioperl, BioSQL, and bioperl-db and uploaded the taxonomy and GO information into BioSQL. I am having a really hard time figuring out how to get the GO information out of the database. If anyone knows the right doc to read or has a simple example program that I could see that would be really useful.

Question 2:

I have collected protein expression data for various states and I would like to cluster the data based on GO information for a start and then if possible use bioperl's ability to analyze mRNA array data to analyze the protein data. Does this seem reasonable? Where should I start looking to figure out how to do this?

Thank you,

Jamie Sherman
Grad Student, UW

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