Remote homology search with hidden Potts models
Fig 5
Hidden Potts model emission probabilities do not match training alignment statistics.
(A) Rfam consensus structure for the class I SAM riboswitch. Base pairs supported by statistically significant covariation in analysis by R-scape in the RF00162 seed alignment are shaded green [41]. (B) Observed pairwise nucleotide frequencies for one base pair in the P3 stem (sites 52 and 62) in our RF00162 benchmark training alignment (192 sequences). (C) Pairwise nucleotide probabilities at sites 52 and 62 under the RF00162 training HPM. (D) Pairwise nucleotide probabilities at sites 52 and 62 under the RF00162 training Infernal pSCFG. Infernal’s informative priors lead to a UG base pair being given significant probability despite being rarely seen in the training data. However, as U is much more common than G at site 52 and vice versa at site 62, Infernal assigns a higher probably to UG than GU at these sites.