[BiO BB] how to get PSSM profile from PSI-BLAST

Martin Gollery marty.gollery at gmail.com
Tue Feb 21 14:12:10 EST 2006

Hi Chan,

To output the profile, use the -C option, as in
blastpgp -d nr -i myfile.faa -C myprofile.ckp -j 3

This will save the profile as myprofile.ckp.


On 2/21/06, chan cheng <siowcheng82 at yahoo.com> wrote:
> I m doing a research about prediction of beta turns in
> proteins from multiple alignment using neural network.
> I had paste the beta turn sequence in PSI-BLAST and
> summit the form. however i cant get the PSSM profile
> that I need it as my neural network input.
> how can i get the profile from PSI-BLAST?
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Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
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