Question

Encoding A Pssm For A Residue

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12.3 years ago

kylejudita ▴ 90

How to encode a PSSM for a residue and present it as feature to the classifier, example would be great.

pssm • 2.0k views

ADD COMMENT • link updated 12.3 years ago by Chris Evelo 10k • written 12.3 years ago by kylejudita ▴ 90

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I edited the keyword to psi-blast instead of psi-plast. If you really meant psi-plast please explain what that is.

ADD REPLY • link 12.3 years ago by Chris Evelo 10k

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Assume that after getting PSSM, am interested to get a value from this matrix for a residue at position 40, what is the value to be extracted from this matrix? is it a vector. then how to use this vector as a feature to be used in a classifier

ADD REPLY • link 12.3 years ago by kylejudita ▴ 90

score 0 · Answer 1 · 2012-07-30

Your question is not very clear, but I think you want to ask how to calculate a position-specific scoring matrix (PSSM) for psi-blast. This is actually done automatically in the first run of psi-blast, see here: http://www.ncbi.nlm.nih.gov/books/NBK2590/

There are quite a few related questions, and yours had probably already been answered. Most are tagged with either psi-blast, psi or pssm.