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   PSSM Viewer Help

What exactly are the PSSM scores and what do they mean?

The scores displayed are log-odds scores, basically calculated as the log (base 2) of the observed substitution frequency at a given position divided by the expected substitution frequency at that position. Thus, a positive score (ratio > 1) indicates that the observed frequency exceeds the expected frequency, suggesting that this substition is surprisingly favored in the CD. A negative score (ratio < 1) indicates the opposite, that the observed substitution frequency is less than the expected frequency, suggesting that the substition is not favored.

See the following for more information on BLAST scoring:
Statistics of Sequence Similarity Scores

BLAST Scoring Parameters