Figure 9

The HMM dynamic programming table is modified to track new count index information at each cell to enable the HMM-with-Duration implementation. The figure shows a view of Viterbi modifications in the dynamic programming table – the transition probabilities are now modified to be a ratio of transition probability cumulants. The transition probability cumulant is calculated based on a predetermined length distribution profile and uses information on the length that is also a (new) cell-level parameter. There are two new cell-level parameters, one each for tracking length on UL and LL states. (For gene-finding, the information to track at the cell-level would be the length of the purported exon, intron, or junk, region.)