[Bioperl-l] Uniprot/Swiss accessions?

[Smithies, Russell]

We re-installed blast version 2.2.18 and everything works perfectly. 
It formats the Uniprot fasta as it should and retrieves sequences with fastacmd as it should.

I think we'll email NCBI and tell them they broke formatdb in their "upgrade"

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Smithies, Russell
> Sent: Tuesday, 19 May 2009 3:43 p.m.
> To: 'bill at genenformics.com'; 'bioperl-l at lists.open-bio.org'
> Subject: Re: [Bioperl-l] Uniprot/Swiss accessions?
> 
> 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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