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

[Martin Heusel]

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

-- 
+ Neural Processing Group Technical University Berlin
+ http://ni.cs.tu-berlin.de
+ Institute of Bioinformatics Johannes Kepler University Linz
+ http://www.bioinf.jku.at/

+ In the beginning was the WORD, and the WORD was UNSIGNED,
+ and the main(){} was without form and void