[Bioperl-l] Trying to find multiple homologs in multiple databases

Jason Stajich jason at bioperl.org
Fri Nov 30 15:21:13 EST 2007


Viktor -
Bio::SearchIO helps you parse BLAST reports, but don't underestimate  
the power of going as low-tech as possible and outputting scores with  
the -m 8 option in NCBI-BLAST or -mformat 3 that give you tabular  
format that is parseable with the 'split' function in Perl.

See the wiki http://bioperl.org/wiki for HOWTOs and examples of using  
the parsers.

You might also consider already-written tools like OrthoMCL,  
InParanoid, and other that help you define relationships like   
orthologs and paralogs among species. There also exist a few  
published web resources that have pre-computed homologs for you,  
might take a look around first unless the point of the project is to  
learn how to run these kinds of searches.

For general Perl help consider Perlmonks.org and some of  the  
introductory books that are available.
-jason
--
Jason Stajich
jason at bioperl.org

On Nov 29, 2007, at 12:20 PM, Viktor Martyanov wrote:

> Hello,
>
> My name is Viktor Martyanov and I am a Ph.D. student in biology at  
> Dartmouth.
>
> I need to be able to use a set of genes or FASTA sequences from S.  
> cerevisiae and retrieve a set of corresponding homologs from other  
> fungal species via BLASTP searches.
>
> I would like to find out if there are Perl scripts that approach  
> this problem. By the way, is there a Perl community or forum where  
> I could post this question?
>
> Thanks very much.  _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l







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