[BiO BB] fastacmd - sequence retreival using "string" ?

[Ryan Golhar]

If you have the FASTA files used to generate the database, why not simply
grep the FASTA file and parse the header that gets returned to you.  This
way, you now have the GI and can use fastacmd to return you the sequence for
that GI.  It may not be the cleanest, but is definitely simple enough.

Ryan
>   
> 
> > -----Original Message-----
> > From:
> > bio_bulletin_board-bounces+mec=stowers-institute.org at bioinform
> > atics.org 
> > [mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at b
> > ioinformatics.org] On Behalf Of Shameer Khadar
> > Sent: Wednesday, January 31, 2007 11:46 AM
> > To: General Forum at Bioinformatics.Org
> > Subject: Fwd: [BiO BB] fastacmd - sequence retreival using 
> "string" ?
> > 
> > Dear Malcom,
> > Thanks for such a detialed  reply !!!
> > I am sorry for the 'bad description' of my problem.
> > 
> > I am aware that fastacmd -s can search using the Accession ID
> > (say a set of
> > numbers ), I am looking for an option to quickly search the 
> > nr database to
> > retreive sequence basesd on the "Query String".
> > 
> > For example : If the following is a snippet of a sequence from nr :
> > > gi|15674171|ref|NP_268346.1,gi|Homo Sapiens - Kinase 1
> > MTHSTCC.....
> > I  need to retrieve the above entries (and of course entries
> > having similar)
> > based on a Query string say "Homo Sapiens". I know this can 
> > be done using a
> > Perl script, and I have coded one for myself, but I need 
> > something quick
> > like fastacmd -s.
> > 
> > Hope you got my question this time.
> > Thanks for all the time you spent for me !!!
> > --
> > Happy Bioinformatics
> > Across the miles... Shameer Khadar
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