[Biodevelopers] getting all db sequences from a PSI-BLAST run

[Martin Heusel]

Hi Noel,

yepp i meant '-e' sorry. For the number of sequences returned i never
get all sequences of a database. Even for a small database with 500
sequences only around 300 are given back. The e-value was set to
1000000. What i recently learned is that blastpgp only makes
approximations for computing the e-values for speed up reasons. It
computes only the first taylor term of a taylor approx. of exp() of

E = K m n exp(-lambda score)

 which only makes sense for not too small scores. So my assumption is
that for to small scores and lambdas the approx. gives way to high
e-values exceeding the -e threshold. By definition an e-value is a
propability and should not go beyond 1.

Regards

  Martin

On 2/25/07, Noel Faux <Noel.Faux at med.monash.edu.au> wrote:
> Hi Martin,
>
> This was probably a typo, but, I think you need '-e' not '-E' to set the
> e-value cutoff for the returned results.  When I wanted all results I
> set -b to the size of the subject database and -e 100000.  The e-value
> never reached that, so PSI-BLAST returned all results.
>
> Cheers
> Noel
>
> Martin Heusel wrote:
> > Hi,
> >
> > i'm wondering if it's possible to get all sequences of a large
> > database ranked by E-value or score from PSI-BLAST with a query.
> > Normally PSI-BLAST stops outputting after a couple of sequences even
> > if one sets the output parameters -b or -E to very high values. Is it
> > possible in general or are there computational limits (time etc.) in
> > figuring out the right scores or E-values when it comes to the many
> > sequences with very low identity? Thanks for any advice.
> >
> > Martin
> >
>
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