dbiblast problem

[Zheng Jin Tu]

Oh ! Yes, my emboss runs same problem.

Before, I find when dbiblast indexed database. seqret is only retrive
first 10000 line of records.  After that give error message.  I have no
idea whether this fixed or not at new emboss releases.

I am now using dbiflat to do that.  It needs flat file instead of fasta
file so more space consuming.

It is my experience.


Thanks,


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


On Fri, 7 Jun 2002, Martin Sarachu wrote:

> yes, I did that before trying dbiblast
>
> martin
>
> Zheng Jin Tu wrote:
> >
> > 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
> > >
>
> --
> Martin Sarachu
> mad at biol.unlp.edu.ar
> EMBnet Argentina
> http://www.ar.embnet.org
>