Resources Learn Page Amino Acid Explorer PSSM Viewer Help CDD Help Go back

What exactly are the PSSM scores and what do they mean? The scores displayed are logodds 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:
