[Biojava-l] log-odds ratio

[Ren, Zhen]

Hi gang,

The WeightMatrixDemo example at "BioJava In Anger" page (http://bioconf.otago.ac.nz/biojava/weightMatrix.htm generates a WeightMatrix from an aligment and uses that matrix to annotate a sequence with a threshold of 0.1.  This program uses the odds, and internally log-odds.  I wonder how I get scores for a sequence by using odds ratio or log-odds ratio, i.e., log(Probability(sequence)/Probability(null model)).  Thanks.

Zhen