afbe9e91a8f837a63978e78e9765ba3e039491ad
larrym
  Mon Jul 5 20:14:58 2010 -0700
add dnaMotifBitScoreWithMarkovBg
diff --git src/inc/dnaMotif.h src/inc/dnaMotif.h
index 793192c..54aecc4 100644
--- src/inc/dnaMotif.h
+++ src/inc/dnaMotif.h
@@ -53,6 +53,13 @@
 double dnaMotifBitScore(struct dnaMotif *motif, DNA *dna);
 /* Return logBase2-odds score of dna given a probabalistic motif. */
 
+double dnaMotifBitScoreWithMarkovBg(struct dnaMotif *motif, DNA *dna, double mark2[5][5][5]);
+/* Return logBase2-odds score of dna given a probabalistic motif using a 2nd-order markov model for the background.
+   motif and markd2 must be in log2 format.
+   Seq must contain an extra two bases at the front (i.e. we start scoring from dna + 2). */
+
+void dnaMotifMakeLog2(struct dnaMotif *motif);
+
 void dnaMotifNormalize(struct dnaMotif *motif);
 /* Make all columns of motif sum to one. */