Create PSI-BLAST PSSM from position-specific weight matrix (probabilities)
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4.0 years ago
M • 0

I have a position-specific weight matrix for a class of protein. Each position has an associated probability for all 20 amino acids being found at that position. How can I convert this weight matrix to a psiblast-compatible PSSM file (to enable use as a query against a sequence database to find sequences that match my profile).

The psiblast PSSM file is the one that starts with:

PssmWithParameters ::= {
pssm {
    isProtein TRUE,
    numRows 28,
    numColumns 20,
    byRow FALSE,
    query seq {

I also welcome suggestions on other methods to search a position-specific weight matrix against a sequence database. I want to be able to make use of the probabilities in the matrix for scoring against the database, not just consider the highest-probability residue at each position. And I'd like to allow for gapped alignment of my profile against target sequences.

Thanks in advance for your help!

psiblast pssm blast • 1.4k views

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