Assessing Variability by Joint Sampling of Alignments and Mutation Rates |
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| Authors: | Dirk Metzler Roland Fleißner Anton Wakolbinger Arndt von Haeseler |
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| Institution: | Johann Wolfgang Goethe-Universit?t, Fachbereich Mathematik, D-60054 Frankfurt am Main, Germany, DE
Max-Planck-Institut für evolution?re Anthropologie, Inselstra?e 22, D-04103 Leipzig, Germany, DE
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| Abstract: | When two sequences are aligned with a single set of alignment parameters, or when mutation parameters are estimated on the
basis of a single ``optimal' sequence alignment, the variability of both the alignment and the estimated parameters can be
seriously underestimated. To obtain a more realistic impression of the actual uncertainty, we propose sampling sequence alignments
and mutation parameters simultaneously from their joint posterior distribution given the two original sequences. We illustrate
our method with human and orangutan sequences from the hyper variable region I and with gene–pseudogene pairs.
Received: 16 November 2000 / Accepted: 15 May 2001 |
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| Keywords: | : Sequence alignment — Markov chain Monte Carlo method — Thorne– Kishino– Felsenstein model — Mutation parameter estimation — Statistical alignment — Hypervariable region — Pseudogenes — Hidden Markov model |
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