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Ancestral Sequence Reconstruction$
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David A Liberles

Print publication date: 2007

Print ISBN-13: 9780199299188

Published to Oxford Scholarship Online: September 2008

DOI: 10.1093/acprof:oso/9780199299188.001.0001

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Probabilistic ancestral sequences based on the Markovian model of evolution: algorithms and applications

Probabilistic ancestral sequences based on the Markovian model of evolution: algorithms and applications

Chapter:
(p.58) CHAPTER 5 Probabilistic ancestral sequences based on the Markovian model of evolution: algorithms and applications
Source:
Ancestral Sequence Reconstruction
Author(s):

Gina M. Cannarozzi

Adrian Schneider

Gaston H. Gonnet

Publisher:
Oxford University Press
DOI:10.1093/acprof:oso/9780199299188.003.0005

A probabilistic sequence (PS) is a sequence in which each position instead of having a single character (amino acid, nucleotide, or codon), has a vector describing the probability of each symbol being the character at that position. A probabilistic ancestral sequence (PAS) is a reconstructed PS for the common ancestor of several sequences. This chapter presents a formalism to compute the probabilities of each character at each position of the biological sequence for the internal nodes in a given phylogenetic tree using a Markov model of evolution. From this model, the probability of an evolutionary configuration can be computed. In addition, efficient algorithms for computing the likelihood score of aligning a character with a character, a character with a probabilistic character, or two probabilistic characters are derived. These scores can then be used in direct string matching or dynamic programming alignments of probabilistic sequences with insertions and deletions. Applications for these alignments, including long-distance homology searching and multiple sequence alignment construction, are shown.

Keywords:   amino acid, nucleotide, codon, phylogenetic tree, Markov model, string matching, dynamic programming, long-distance homology

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