[BiO BB] Parameter -e blastpgp/PSI-BLAST

[Martin Gollery]

Correct. The -h option affects what sequences are allowed in building the
PSSM, and -e affects the final alignment threshold. This is a useful thing,
because you might typically want a more lenient threshold with -h to
maximize the entropy of the PSSM, while keeping -e more stringent so that
you don't get a million crummy hits at the end.


Marty

On 5/2/06, Martin Heusel <mheusel at gmail.com> wrote:
>
> On 5/2/06, Martin Gollery <marty.gollery at gmail.com> wrote:
> > -e sets the threshold expectation value for alignments in the final
> output.
> > -h is the threshold for inclusion into the PSSM. I believe the default
> > setting for -e is 10, which is extremely lenient.
>
> Hi Marty,
>
> is it correct then that -e doesn't affect a PSSM at the end of some
> iterations?
>
> regards
>
> Martin
>
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--
--
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
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