[Biopython] NCBIWWW.qblast Expect value / E-value

[Jasper Koehorst]

Yes we have, at the moment are we trying to identify a lot of small peptides
in several organisms for a project. What we would like to do is to ignore
the e-value for this moment. But a solution has yet to be found.
jasper koehorst


2009/5/20 Peter Cock <p.j.a.cock at googlemail.com>

> On Wed, May 20, 2009 at 1:51 PM, Jasper Koehorst
> <jasperkoehorst at gmail.com> wrote:
> > Im running against problems when i try to identify short peptide
> sequences
> > of ±10 - 20 peptides. When i run this at the NCBI Blast website i get
> > results, these all have
> > high E-Values that i dont really care at the moment. The problem is when
> i
> > do this in biopython as stated below, i will not get any results...
> >
> > I believe this is due to the fact that biopython will not show results
> with
> > a "high" E-Value. Is there a way to change this? So it will allow results
> > with an E-value of ±1500 or more?
>
> Nothing in Biopython limits the expectation values - our qblast function
> defaults to 10, but you can set this to what you like. However, the NCBI
> may be imposing their own limit. Are you sure using anything more than
> 10 is actually meaningful?
>
> > I tried the sript below but that does not quit work...
> >
> > Anybody has an idea?
> >
> >        result_handle =
> > NCBIWWW.qblast("blastp","nr",peptide[1],entrez_query=i, expect=2000,
> > matrix_name='BLOSUM80')
> >        blast_records = NCBIXML.parse(result_handle)
> >        blast_record = blast_records.next()
> >        E_VALUE_TRESH = 10000000
> >        for alignment in blast_record.alignments:
> >            for hsp in alignment.hsps:
> >
>
> I would guess (from previous examples) that this is due to the NCBI
> website and QBLAST API using different default parameters - the
> NCBI likes to change the defaults on the website from time to time,
> and these may differ from what you are getting via their QBLAST
> API. I would start by checking the gap parameters.
>
> See also:
> http://lists.open-bio.org/pipermail/biopython/2008-May/004252.html
> http://lists.open-bio.org/pipermail/biopython/2007-August/003679.html
>
> Peter
>