TY - JOUR AU - Ezawa, Kiyoshi PY - 2016 DA - 2016/09/27 TI - General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation JO - BMC Bioinformatics SP - 397 VL - 17 IS - 1 AB - Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a method to reliably calculate the occurrence probabilities of sequence alignments via evolutionary processes on an entire sequence. Previously, we presented a perturbative formulation that facilitates the ab initio calculation of alignment probabilities under a continuous-time Markov model, which describes the stochastic evolution of an entire sequence via indels with quite general rate parameters. And we demonstrated that, under some conditions, the ab initio probability of an alignment can be factorized into the product of an overall factor and contributions from regions (or local alignments) delimited by gapless columns. SN - 1471-2105 UR - https://doi.org/10.1186/s12859-016-1167-6 DO - 10.1186/s12859-016-1167-6 ID - Ezawa2016 ER -