dbiblast problem

[john walshaw (JIC)]

I have experienced a similar problem, tring to index WU-BLAST-formatted databases with
dbiblast. However I got it to work properly with NCBI-BLAST-formatted databases.

John Walshaw, John Innes Centre, Norwich Research Park,
Colney, Norwich NR4 7UH, UK. +44(0)1603 450827

> -----Original Message-----
> From: David.Bauer at SCHERING.DE [mailto:David.Bauer at SCHERING.DE]
> Sent: 26 June 2002 12:32
> To: emboss at embnet.org
> Subject: dbiblast problem
> 
> 
> Hi,
> 
> I observed the folowing problem when retrieving entries from 
> blast databases
> formated with dbiblast:
> 
> I get the CORRECT sequence if I specify the ID:
> --------------------------------------------------------------
> ---------------------------------------------------------------
> seqret -auto -stdout cgdb_nt:celsl2a
> >CELSL2A M27263 C.elegans trans-spliced leader 2 (SL2 
> RNA-alpha) gene, 5' flank.
> seqret -auto -stdout cgdb_nt:celsl2b
> >CELSL2B M27264 C.elegans trans-spliced leader 2 (SL2 
> RNA-beta) gene, 5' flank.
> ##############################################################
> ###########
> 
> But I get the WRONG sequences if I specify the ACC:
> --------------------------------------------------------------
> ----------------------------------------------------------------
> seqret -auto -stdout cgdb_nt:M27263
> >CELSL2B M27264 C.elegans trans-spliced leader 2 (SL2 
> RNA-beta) gene, 5' flank.
> seqret -auto -stdout cgdb_nt:M27264
> >CELSNTI L15302 C.elegans synaptotagmin I mRNA, complete cds 
> and flanking
> regions.
> ##############################################################
> #############
> 
> With fastacmd the headers look like this:
> --------------------------------------------------------------
> -------------------------------------------------------------------
> >gb|M27263|CELSL2A C.elegans trans-spliced leader 2 (SL2 
> RNA-alpha) gene, 5'
> flank
> >gb|M27264|CELSL2B C.elegans trans-spliced leader 2 (SL2 
> RNA-beta) gene, 5'
> flank
> ##############################################################
> ############
> 
> Any ideas ?
> 
> Thanks, David.
> 
>