[Bioperl-l] Finding all human paralogues

[Torsten Seemann]

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; 

-- 
Torsten Seemann <torsten.seemann at infotech.monash.edu.au>
Victorian Bioinformatics Consortium