[Bioperl-l] 2 psi-blast questions

[Andreas Bernauer]

Donald G. Jackson wrote:
> Hadas Leonov wrote:
> >I noticed that a psi-blast report only considers new hits if the 0.0 < 
> >E-value < 0.01 (?).
> >Is there any possibility to change these parameters ? especially the 
> >0.0 limit, cause large query sequences with 60% identity might still 
> >give an e value of 0.0, thereby causing me to miss them completely by 
>
> You can set the -h value ($blaster->h()) to adjust the inclusion 
> threshold for refining the scoring matrix.  However, it only takes 
> expect values - not identity/length - and the expect value can't go 
> below zero.  

I think he meant that evalues that are exactly zero get excluded, as
the threshold is tested with a "lower than" (`<') instead of an "lower
or equal than" (`<=').

Andreas.