title: Estimation and reliability of molecular sequence alignments.
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.
authors.affiliation: Biometrics Unit, Cornell University, Ithaca, New York 14853, USA.
authors.forename: J L
authors.initials: JL
authors.lastname: Thorne
authors.forename: G A
authors.initials: GA
authors.lastname: Churchill
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D001699:Biometry / Q000379:methods; D008433:Mathematics; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011336:Probability; D013269:Stochastic Processes