[Bioperl-l] p-value, e-value

[Jason Stajich]

I'm implementing the Bio::Search::HSP::GenericHSP and
Bio::Search::Hit::GenericHit objects, wanted to clarify our use of e-value
and p-value.  I think we have been interchanging them and considering p
and alias of evalue.  Is that indeed the correct behavior we should be
exhibiting?  Do we need to have separate data fields to store these or
will they be equivalent in all HSP contexts?

In BLAST we have an 'Expect' value in the HSP and a significance value the
Hit.

In FASTA we have an E() value in the Hit description and an E() value in
the HSP.

In HMMer we have an E-value in both the HSP and the Hit.

Thanks.
-jason

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu