[EMBOSS] index RefSeq for EMBOSS

Wells, Isabelle isabelle.wells at roche.com
Fri Apr 21 11:43:27 EDT 2006


Yes I also index refseq. I think the problem here is that dbiflat can only handle files which are less than 2GB. So try splitting the files first.


-----Original Message-----
From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Olivier Friard
Sent: Friday, April 21, 2006 17:00
To: emboss at emboss.open-bio.org
Subject: [EMBOSS] index RefSeq for EMBOSS


I tried to index the RefSeq database:

1) I downloaded all 
file (GB format)

2) gunziped

3) Added the rs_dna entry to my .embossrc file

DB rs_dna [
    type: "N"
    method: "emblcd"
    format: "GB"
    dir: "/home/users/friard/data/refseq_genomic/"
    file: "*.gbff"
    release: ""
    comment: "RefSeq Genomic  (upd)"
    indexdir: "/home/users/friard/data/refseq_genomic/"

4) used dbiflat with following arguments (from the directory where files 
are stored)

Index a flat file database
Database name: rs_dna
       EMBL : EMBL
      SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
         GB : Genbank, DDBJ
     REFSEQ : Refseq
Entry format [SWISS]: REFSEQ
Database directory [.]:
Wildcard database filename [*.dat]: *.gbff
Release number [0.0]:
Index date [00/00/00]:

The indexes were created but when I try to access to a sequence (i.e 
seqret rs_rna:NC_000004) then results is not the correct sequence but an 
other one with the NC_000004 ID!

I also downloaded the file in FASTA format and tried to index them with 
the dbifasta command (format: ncbi) without positive results:

seqret rs_dna:nc_000004
Reads and writes (returns) sequences
Error: Unable to read sequence 'rs_dna:nc_000004'
Died: seqret terminated: Bad value for '-sequence' and no prompt

Does anyone index the RefSeq successfully?
Thank you in advance


Olivier Friard
Laboratorio di Biologia Computazionale
Facoltà di Scienze MFN
Università di Torino
via Accademia Albertina 13, 10124 TORINO (Italy)

tel. +39 011 6704689

EMBOSS mailing list
EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss

More information about the EMBOSS mailing list