[EMBOSS] Using seqret to fetch from .nal index databases

[Ryan Golhar]

If you are using a NCBI formatted database, why not just use formatseq
from the ncbi toolkit to extract the sequence?



-----Original Message-----
From: emboss-bounces at emboss.open-bio.org
[mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of Audra Johnson
Sent: Friday, July 29, 2005 3:09 PM
To: emboss at emboss.open-bio.org
Subject: [EMBOSS] Using seqret to fetch from .nal index databases


Apologies for the length, but I want to be thorough.  I'm doing blast  
searches and then trying to fetch the sequences from the our genembl  
database using seqret.  For example:

blastall -p tblastn /gcgdata_10.3/gcgblast/genembl -i  
dp00061_disordered_115_168.fasta

Gives me results of:

GB_PR:HUMRPA70KD        2e-08   412     573     1       54      54
GB_PR:BC018126  2e-08   386     547     1       54      54
GB_PAT:AX335048 2e-08   412     573     1       54      54
GB_PAT:AR175924 2e-08   412     573     1       54      54
GB_RO:BC019119  0.003   399     584     1       53      62

I've tried using a seqret just for the database name I'm giving  
blastall, and specifically saying the genembl.nal file:

$ seqret
Reads and writes (returns) sequences
Input sequence(s): /gcgdata_10.3/gcgblast/genembl.nal:HUMRPA70KD
Error: Unable to read sequence '/gcgdata_10.3/gcgblast/ 
genembl.nal:HUMRPA70KD'
Input sequence(s): /gcgdata_10.3/gcgblast/genembl:HUMRPA70KD
Error: failed to open filename '/gcgdata_10.3/gcgblast/genembl'
Error: Unable to read sequence '/gcgdata_10.3/gcgblast/ 
genembl:HUMRPA70KD'
Died: seqret terminated: Bad value for '-sequence' and no more retries

But neither works.  (I've omitted the beginning prefix GB_PR: and  
similar prefixes, but I've tried that way and it doesn't work,  
either.)  Is there any way to get seqret functioning with these  
databases?

-- Audra Johnson, University of Idaho
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