What is a PSSM ?
A PSSM is a Position Specific Scoring Matrix. A profile is one type of PSSM.
PSSMs enable the scoring of multiple alignments with sequences, structures etc.
There are a number of ways to convert a multiple alignment, such as a block,
into a PSSM. The conversion can use the multiple alignment sequence weights,
the expected number of amino acids and the frequencies of unobserved amino
More information on PSSMs can be found in the
Lastly, PSSM is pronounced "possum".
Page last modified May 1996