[Bioperl-l] Uniprot/Swiss accessions?

[Smithies, Russell]

There's no descriptions in the top of the blast output and no accessions in the alignments.
The fasta is coming from UniProt so surely they know how to format files.
And it does match what NCBI require in their defline i.e. 	sp|accession|entry name

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of bill at genenformics.com
> Sent: Tuesday, 19 May 2009 3:13 p.m.
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Uniprot/Swiss accessions?
> 
> I could not see the difference.
> 
> Do you follow the rules for FASTA defline:
> 
> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.table.632
> 
> Bill
> 
> 
> > No, that doesn't work :-(
> > Here's some blast output with the database formatted with local ids:
> > =====================================================================
> > Database: uniprot_sprot.fasta
> >            466,739 sequences; 165,389,953 total letters
> >
> > Searching..................................................done
> >
> >
> >
> >                                                                  Score
> > E
> > Sequences producing significant alignments:                      (bits)
> > Value
> >
> > sp|Q4U9M9|104K_THEAN Unknown                                          421
> >  e-117
> > sp|P15711|104K_THEPA Unknown                                          265
> >  6e-70
> > sp|Q2SPQ2|CHED_HAHCH Unknown                                           33
> >  4.2
> >
> >
> >  Score =  421 bits (1083), Expect = e-117,   Method: Compositional matrix
> > adjust.
> >  Identities = 0/209 (0%), Positives = 0/209 (0%)
> >
> > Query: 1   VHKVVEGDIVIWENEEMPLYTCAIVTQNEVPYMAYVELLEDPDLIFFLKEGDQWAPIPED 60
> >
> > Query: 61  QYLAXXXXXXXXIHTESFFSLNLSFQHENYKYEMVSSFQHSIKMVVFTPKNGHICKMVYD
> > 120
> >
> > Query: 121 KNIRIFKALYNEYVTSVIGFFRGLKLLLLNIFVIDDRGMIGNKYFQLLDDKYAPISVQGY
> > 180
> >
> > Query: 181 VATIPKLKDFAEPYHPIILDISDIDYVNF 209
> >
> > ===========================================================================
> >
> > If I tweak the fasta and change the ids from lcl to gi and re-formatdb,
> > all works correctly:
> >
> > ===========================================================================
> > Query= test
> >          (612 letters)
> >
> > Database: uniprot_sprot.fasta
> >            466,739 sequences; 165,389,953 total letters
> >
> > Searching..................................................done
> >
> >
> >
> >                                    %2
> 
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