Multiple sequence alignment: Difference between revisions

Revision as of 18:48, 18 May 2020

Revision as of 22:22, 24 May 2020

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===Hidden Markov models===

[[File:A profile HMM modelling a multiple sequence alignment.png|thumb|A profile HMM modelling a multiple sequence alignment]]

[[Hidden Markov model]]s are probabilistic models that can assign likelihoods to all possible combinations of gaps, matches, and mismatches to determine the most likely MSA or set of possible MSAs. HMMs can produce a single highest-scoring output but can also generate a family of possible alignments that can then be evaluated for biological significance. HMMs can produce both global and local alignments. Although HMM-based methods have been developed relatively recently, they offer significant improvements in computational speed, especially for sequences that contain overlapping regions.<ref name="mount" />