DNA training data simulation results. Each row in (a) and set of bars in (b) corresponds to a different conservation level in the 4 "true profiles". The first column and the top bar (white) depicts the average log-probability of the training sequences using the 16 starting profiles. The second (amber) depicts the average log-probability of the training sequences using the true profiles. The third (red) depicts the average log-probability using the Baum-Welch (BW) algorithm. The fourth (blue) depicts using the Conditional Baum-Welch (CBW) algorithm. The fifth (yellow) depicts using the Dynamic Model Surgery (DMS) algorithm with the BW algorithm, and the sixth (green) depicts using the CBW and DMS algorithms together. All bars in (b) have been shifted so that the lowest bar is at 0. The new algorithms all outperform BW at conservation levels above .6. At .5 and below, CBW does not outperform BW. At the highest levels, both algorithms employing DMS perform equally well.
Edlefsen and Liu BMC Genomics 2010 11(Suppl 1):S10 doi:10.1186/1471-2164-11-S1-S10