[EMBOSS] difficulty using databases and "water"

Scott Markel smarkel at scitegic.com
Fri Sep 10 17:23:24 UTC 2004

I'm using 2.9.0, built in cygwin, running in Windows XP.
I'm having problems creating databases for use with "water".

I created a USA database using dbifasta.

133 > dbifasta -idformat idacc -directory /C/SandBox/EMBOSS -filenames NRDB_protein_10.* -dbname NRDB_protein_10 -release 1.0 -date "10/09/04" -fields acnum -fields des -fields seqvn
Index a fasta database

I edited ~/.embossrc to include the new database.

134 > cat ~/.embossrc
DB NRDB_protein_10 [
    type: P
    format: fasta
    method: emblcd
    fields: "id acc sv des"
    directory: /C/SandBox/EMBOSS
    indexdirectory: /C/SandBox/EMBOSS
    file: NRDB_protein_10.fa

showdb does the right thing.

135 > showdb
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
NRDB_protein_10 P    OK  OK  OK  -

seqret can access all of the database.

136 > seqret NRDB_protein_10:\* stdout
Reads and writes (returns) sequences
 >XP_357594.1 XP_357594.1 similar to KIAA0960 protein [Mus musculus]
<shows all 10 sequences just fine>

I can't seem to access an individual sequence.

137 > seqret NRDB_protein_10:XP_357594
Reads and writes (returns) sequences
Error: Unable to read sequence 'NRDB_protein_10:XP_357594'
Died: seqret terminated: Bad value for '-sequence' and no prompt

What I'm really trying to do is run "water", but I expect
my database problems are impacting that.

161 > water -asequence query.fa -bsequence NRDB_protein_10:\*
Smith-Waterman local alignment.

    EMBOSS An error in ajarr.c at line 1805:
Token missing

Any pointers to documentation or examples would be greatly


Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at scitegic.com
SciTegic Inc.                       mobile: +1 858 205 3653
9665 Chesapeake Drive, Suite 401    voice:  +1 858 279 8800, ext. 253
San Diego, CA 92123                 fax:    +1 858 279 8804
USA                                 web:    http://www.scitegic.com

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