[Bioperl-l] Reading all sequences using Bio::DB::Flat in SwissProt file

[Daily, Kenneth Michael]

I want to work with a local copy of the SwissProt database, and need to search through all of the entries. I only see methods to return sequences by accession. However, I cannot use just FASTA format of the SwissProt records, as I need to use the feature fields. What I need to learn is how to do a DB search on the features field of the SwissProt records, if its possible. Would there be any advantage do doing it with the DB instead of just using SeqIO as an input stream? I think it might, since every time I want to do a search I must read in the entire file again, which is very costly. Thank you.

Kenny Daily
Indiana University
School of Informatics
kmdaily [at] indiana [dot] edu