Estimation and reliability of molecular sequence alignments.

J L Thorne; G A Churchill

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PubMed · 7766767

Estimation and reliability of molecular sequence alignments.

J L Thorne·G A Churchill

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Abstract

The problem of estimating the relatedness of a pair of biological sequences is addressed. A stochastic model of sequence evolution is described that allows insertion and deletion as well as replacement of amino acid residues (or substitution of nucleotides) over time. An expectation-maximization (EM) algorithm that obtains maximum likelihood estimates of the model parameters is introduced. The method assumes that the sequences are related by descent from a common ancestor but the alignment (i.e., the precise evolutionary correspondence between residues in each sequence) is unknown. Results from the E-step of the EM algorithm are used to assess the likelihood that any two residues are related by direct descent from a common ancestor.

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Algorithms Amino Acid Sequence Animals Base Sequence Biological Evolution Biometry Mathematics Models, Genetic Models, Statistical Molecular Sequence Data Probability Stochastic Processes Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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J L Thorne, G A Churchill. 1995. Estimation and reliability of molecular sequence alignments.. https://pubmed.ncbi.nlm.nih.gov/7766767/

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