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

[Sean Davis]

Kenny,

If this is something you are going to be doing often, you might want to 
look at bioperl-db.  Alternatively, UCSC maintains a fully-relational 
swissprot database 
(http://hgdownload.cse.ucsc.edu/goldenPath/swissProt/database/) that 
you could pretty easily load into a mysql server.  You can access their 
mysql server directly (let me know if you want to do this), also, but 
if you are running any kind of batch query, I would suggest you 
download the tables and load them yourself (really pretty easy to do).

Sean

On Jan 19, 2005, at 11:48 AM, Daily, Kenneth Michael wrote:

> 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
>
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