[Biocorba-l] Re: [Bioperl-l] Parsing the accession numbers in Refseq

[Ewan Birney]

On Tue, 15 May 2001, Suraj Peri wrote:

> hi,
>  I have a set of Fasta format files protein sequences.
> I now want all these to be qued automatically to
> either Pfam or SMART server. Right now, in Pfam and
> SMART we have to paste only one sequence. But how can
> i automate if i have to send all the FASTA format file
> once and get the outputs in one click. 


I suggest you download the HMMER package and run it locally for both Pfam
and SMART (at least for Pfam this is doable). Follow instructions from
pfam.wustl.edu or www.sanger.ac.uk/Software/Pfam


Please try to refrain from using remote web servers as a subsititute for
running batch jobs - use your own compute for that.



>     Can this be done using PERL (Windows OS) . if so
> how . Please help me group!!
> Thank you
> SP
> dk
>  
> 
> __________________________________________________
> Do You Yahoo!?
> Yahoo! Auctions - buy the things you want at great prices
> http://auctions.yahoo.com/
> _______________________________________________
> Biocorba-l mailing list
> Biocorba-l@biocorba.org
> http://www.biocorba.org/mailman/listinfo/biocorba-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------