[Bioperl-l] Finding seqs of given domain architecture

Dave Messina David.Messina at sbc.su.se
Wed Apr 16 14:23:27 EDT 2008


Hey Jacob,

This forum is mostly geared toward the BioPerl software package rather than
general bioinformatics assistance.

That being said, I would recommend using Pfam's Sequence Search to determine
the domain content of your sequences and then simply looking at those which
have the same two domains of interest.

If there are more sequences matching this criterion than can be examined
manually, you could write up something (potentially using BioPerl) to then
look at the relative order and number of those domains in your sequences.

However, if these sequences have UniProt IDs, you can start with the domains
and Pfam will hand you a list of all the UniProt seqs having those domains.
On the Pfam website's main page, click on "Help" (right side of menu at the
top of the page) and then "Tools and Services" (left side menu).


Dave


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