[Bioperl-l] Command-line Psiblast using NCBI blastpgp

Xiang Deng xiang.deng at duke.edu
Mon Feb 23 10:37:50 EST 2004

Hi Everyboday,

I got a question about how to do psiblast using NCBI blastpgp. The thing I 
want to do is to use a PSSM generated from a multiple alignment of our 
internal data to blast against NCBI nr database. I followed the 
instruction from blast tutorial as follows,

blastpgp -i seq1.txt -B align.msf -e 5000 -F F -j 2 -v 10 -d nr -o 
test_out.txt -C pssm.txt

I do not know why I have to specify a single sequence in seq1.txt from the 
aligned sequences in align.msf. I want to use the pssm created from the 
multiple alignment in align.msf to blast instead of only one sequence. And 
the result looks like using the single sequence only for blast and I could 
not see any sign of using the PSSP calculated from the multiple alignment. 
I am concerned about that result, does anyone have the same experience and 
know what is going on there? whether or not the command-line above did 
exactly what I want and Iam just too suspicious? 

And anyone has a better way to do this kind of psiblast via command-line?

thanks a lot,


Department of Pharmacology and Cancer Biology
Duke University Medical Center
Durham, NC 27710

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