Questions about PSI-Blast and PSSM

[Shunrei]

Hi!

I have 2 questions about PSI-Blast/blastpgp.

1/ I can get a PSSMWithParameters file on the PSI-Blast NCBI website.
This file contains both intermediate data and final data:

intermediateData {
freqRatios {
{ 0, 10, 0 },
{ 35613, 10, -6 },
...
{ 0, 10, 0 }
}
},
finalData {
scores {
-32768,
-2,
...
-4
},
lambda { 0, 10, 0 },
kappa { 508343, 10, -7 },
h { 0, 10, 0 }
}
}
}
(end of file)

However, with blastpgp, my PSSMWithParameters file contains only the
intermediate data (= no final data and kappa lambda h). And I cannot
use this file for the "upload PSSM" option on the PSI-BLAST NCBI
website. My first question is : how can I obtain the "complete" file
with blastpgp?


2/ I've installed the standalone WWW Blast server suite of programs,
but I don't know how I can save the PSSM when I run a PSI-Blast
search. Is it possible to save it?


Hope you can help me! :-)

Shunrei