Align a position-specific weight matrix against a sequence database
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2.9 years ago
M • 0

I am looking for methods to search a n x 20 position-specific weight matrix against a FASTA sequence database. My weight matrix describes a protein of length n. For each position in the protein 1...n, I know the probabilities that each of the 20 possible amino acid (A,C,D-W) exists at that position, with probabilities summing to 1. 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.

Tool suggestions, and example code are highly appreciated. Thanks!

PWM Protein PSSM HMM • 913 views
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