[Bioperl-l] Uniprot/Swiss accessions?
bill at genenformics.com
bill at genenformics.com
Tue May 19 03:13:19 UTC 2009
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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