[Bioperl-l] Finding all human paralogues

[Yuval Itan]

Many thanks Torsten, that greatly helps!

Yuval

On Wednesday 15 March 2006 01:52, you wrote:
> Yuval,
>
> > -------------------- WARNING ---------------------
> > MSG: cannot find path to blastall
> > ---------------------------------------------------
> > Can you suggest how to solve that?
>
> Have you installed the blast binaries?
> Are they in your $PATH?
> Have you created a $HOME/.ncbirc file?
>
> Please read http://www.ncbi.nlm.nih.gov/blast/docs/
> and http://doc.bioperl.org/bioperl-live/Bio/Tools/Run/StandAloneBlast.html
>
> > Also, I would like to have the Blastp function inside my own programme.
> > Is there any available source code for that?
>
> BLAST is part of the NCBI toolkit:
> http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
>
> > my $human_genes = $comparadb->get_MemberAdaptor->fetch_by_source_taxon(
> >         'ENSEMBLGENE', 9606); # getting all human genes
> > my @params = (program  => 'blastp', database => $human_genes, _READMETHOD
> > => 'SearchIO' );
>
> 'database' has to be the name of the database of sequences to blast
> against. This has to exist as a set of blast index files on your disk.
> The 'formatdb' program can be used to create this. You appear to be
> passing some Perl object instead?
>
> Please read http://www.ncbi.nlm.nih.gov/blast/docs/
>
> > my $blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);
> > my $seq_obj = Bio::Seq->new(-id  =>"test query", -seq
> > =>$human_genes->[$i]->get_longest_peptide_Member()->sequence);
> > my $report_obj = $blast_obj->blastall($seq_obj);
>
> die "unable to blastall" if not defined $report_obj;
>
> > my $result_obj = $report_obj->next_result;
>
> die "no result found" if not defined $result_obj;