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Regional Context in the Alignment of Biological Sequence Pairs

Sammut, Raymond; Huttley, Gavin Austin


Sequence divergence derives from either point substitution or indel (insertion or deletion) processes. We investigated the rates of these two processes both in protein and non-protein coding DNA. We aligned sequence pairs using two pair-hidden Markov models (PHMMs) conjoined by one silent state. The two PHMMs had their own set of parameters to model rates in their respective regions. The aim was to test the hypothesis that the indel mutation rate mimics the point mutation rate. That is, indels...[Show more]

CollectionsANU Research Publications
Date published: 2011
Type: Journal article
Source: Journal of Molecular Evolution
DOI: 10.1007/s00239-010-9409-0


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