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

[Noel Faux]

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
>