[Bioperl-l] Are frac_identical and frac_conserved methods for hit or for hsp objects?

Jason Stajich jason.stajich at duke.edu
Tue Feb 28 13:31:00 UTC 2006

Personally, I only use these values from HSPs - the Hit methods  
require HSPs to be tiled to summarize the bases and I'm not convinced  
the method works for all situations.

If you want it summarized to a single value for query/hit pair I  
would use FASTA or use WU-BLAST to if you must use BLAST, get the  
links path out and summarize it on a set of HSPs paths.

On Feb 28, 2006, at 7:17 AM, Javier Forment wrote:

> Hi bioperlers... I have some questions when parsing BLAST results.
> As far as I know, bioperl documentation for Bio::SearchIO states that
> frac_identical and frac_conserved are methods for hsp objects (e.g.,
> $hsp->frac_identical). I have found that it is also possible to use
> these methods for hit objects (e.g., $hit->frac_identical), since it
> does not give an error, but in this case they don't work properly (I
> think that they work fine with blastn, but not with blastx). So my
> questions are:
> 1.- is it right to use $hit->frac_identical and $hit->frac_conserved?
> 2.- if so, how they get the frac_identical for a hit when it has more
> than one HSP (maybe getting the average value for all the hsps)?
> 3.- if so, why they don't work fine sometimes, for example, with  
> blastx?
> 4.- if not, is there any method to get the fraction of identical or
> conserved residues for a hit, other than averaging the corresponding
> values for all the hsps of this hit?
> Thanks a lot in advance,
> Javier.
> -- 
> Javier Forment Millet
> Unidad de Bioinformatica del Laboratorio de Genomica
> Instituto de Biologia Molecular y Celular de Plantas
> Universidad Politecnica de Valencia
> Avenida de los Naranjos, s/n
> 46022 Valencia (Spain)
> Tlf.(1): +34-963877885
> Tlf.(2): 685142553
> FAX: +34-963877859
> e-mail: jforment at ibmcp.upv.es
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Jason Stajich
Duke University

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