dbiblast problem

[Zheng Jin Tu]

You may need to run formatdb first then run dbiblast.

formatdb -i input_seq -p T -o T      (for nucleic acid)
formatdb -i input_seq -p F -o T      (for protein)

Thanks,


Tu
============================================================


On Fri, 7 Jun 2002, Martin Sarachu wrote:

> Hi,
>
> anyone found a solution for the dbiblast problem?
>
> I'm trying to index the formatdb'ed humrep.fas (nuc) FASTA database
>
> > % dbiblast
> > Index a BLAST database
> > Database name: humrep.fsa
> > Database directory [.]:
> > Wildcard database filename [humrep.fsa]: humrep.fsa.*
> > Release number [0.0]:
> > Index date [00/00/00]:
> >          N : nucleic
> >          P : protein
> >          ? : unknown
> > Sequence type [unknown]: N
> >          1 : wublast and setdb/pressdb
> >          2 : formatdb
> >          0 : unknown
> > Blast index version [unknown]: 2
> >
> >    EMBOSS An error in dbiblast.c at line 640:
> >  cannot open ./humrep.fsa.nhr table file ./humrep.fsa.nhr.nin
>
>
> I also get a similar error when trying with nr (prot) database
>
> > $ dbiblast
> > Index a BLAST database
> > Database name: nr
> > Database directory [.]:
> > Wildcard database filename [nr]: nr.*
> > Release number [0.0]:
> > Index date [00/00/00]:
> >          N : nucleic
> >          P : protein
> >          ? : unknown
> > Sequence type [unknown]: P
> >          1 : wublast and setdb/pressdb
> >          2 : formatdb
> >          0 : unknown
> > Blast index version [unknown]: 2
> >
> >    EMBOSS An error in dbiblast.c at line 640:
> >  cannot open ./nr.phr table file ./nr.phr.pin
>
>
> martin
>
> --
> Martin Sarachu
> mad at biol.unlp.edu.ar
> EMBnet Argentina
> http://www.ar.embnet.org
>