[EMBOSS] can't access databases indexed by dbifasta

[Gary Williams, Tel 01223 494522]

David Martin wrote:
> 
> On 17/2/04 3:23 pm, "Marcus Claesson" <m.claesson at student.ucc.ie> wrote:
> 
> > Hi,
> >
> > I have now changed emboss/emboss.defaults to:
> >
> > SET $emboss_db_dir /var/data/blast_db
> >
> > DB ecoli.nt [
> >  type: "N"
> >  format: "fasta"
> >  method: "emblcd"
> >  dir: "$emboss_db_dir"
> >  indexdir: "$emboss_db_dir"
> >  file: "ecoli.nt"
> > ]
> >
> > And get the same negative result:
> >
> > [marcus]$ showdb
> > Displays information on the currently available databases
> > # Name        Type ID  Qry All Comment
> > # ====        ==== ==  === === =======
> > ecoli.nt      N    OK  OK  OK  -
> >
> > [marcus]$ seqret ecoli.nt
> 
> 'seqret ecoli.nt:\*' perhaps?

That would be more explicit and clearer for other people to read, but a
database-name on its own is a perfectly legal EMBOSS USA.

Try: 'seqret embl'

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk