Mutual Information

Mutual Information between i and j
- measure correlation
- covariation of nucleotides
- 0 means i and j are independent = p(i,j) = p(i)p(j)
- useful for Covariance Models (CM) in RNAFolding (eg. RNAalifold - Hofacker et al. JMB 2002, 319:1059-1066)

http://nlp.stanford.edu/IR-book/html/htmledition/mutual-information-1.html#mifeatsel2

http://mendel.informatics.indiana.edu/~yye/lab/teaching/get.php?course=fall2010-I519&name=RNAfold.pdf