Applying A Pssm To Psi-Blast
Entering edit mode
11.9 years ago

I'm able to generate a PSSM and a sequence from combinatorial experimental data. I want to BLAST the results to find proteins displaying these motifs. However, I have information about each position's sensitivity to substitutions, in addition to a consensus sequence. I know how to create a PSSM from this information, but I don't know how to incorporate this into a BLAST search. Does anyone know a cmdline argument to blast or a way of hacking a PSSM into a PSI-BLAST search to add position information to a sequence?

pssm blast • 3.7k views
Entering edit mode
11.9 years ago

You might find some information in this post :

As well as here : and here

What you probably need to do:

  • generate a .chk checkpoint file similar to the one generated by 'blastpgp' containing your PSSM
  • feed it to blastpgp with something similar to:

    blastpgp -i test1.fa -d genome.faa -R test1.chk -o -I T -a 2


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