[Bioperl-l] Uniprot/Swiss accessions?

[bill at genenformics.com]

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