[Bioperl-l] Uniprot/Swiss accessions?

[Bernd Web]

Hi Russel,

Thanks for posting this issue. I have the same problem  with formatdb
from 2.2.19. When using my older still installed 2.2.17 everything was
fine again :)
So you were lucky to revert from to 2.2.18.


Regards,
Bernd

On Tue, May 19, 2009 at 5:54 AM, Smithies, Russell
<Russell.Smithies at agresearch.co.nz> wrote:
> 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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