Lecture Notes: Markov chains
نویسنده
چکیده
In considering the degree of similarity that we expect by chance, these scoring functions allow us to compare two alignments by comparing their scores, but are less useful for assessing a pairwise alignment in an absolute sense. Given a pair of aligned sequences with a particular collection of matches, mismatches, and indels, does the alignment reflect enough similarity to suggest that it is of biological interest? One way of assessing an alignment in an absolute sense is to determine whether it reflects more similarity than we would expect by chance. In developing this approach, we must take into account the divergence of related sequences due to mutation. With that in mind, we will explore models of sequence evolution and then discuss how they are used to assess alignments. Sequence evolution models are typically based on Markov chains, so we will begin with a general introduction to Markov models.
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