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

[Javier Forment]

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