[Bioperl-l] Are frac_identical and frac_conserved methods for hit or for hsp objects?
jforment at ibmcp.upv.es
Tue Feb 28 12:17:59 UTC 2006
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
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 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)
e-mail: jforment at ibmcp.upv.es
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