dbiblast problem

David.Bauer at SCHERING.DE David.Bauer at SCHERING.DE
Wed Jun 26 11:32:22 UTC 2002


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.





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