A context dependent pair hidden Markov model for statistical alignment

DOI10.2202/1544-6115.1733MaRDI QIDQ2921246zbMATH OpenOpenAlexWikidataFDO

Authors Ana Arribas-Gil, Catherine Matias

Publication date 8 October 2014

Published in Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1107.2798

zbMATH Keywords

comparative genomicscontextual alignmentDNA sequence alignmentEM algorithminsertion deletion modelpair hidden Markov modelprobabilistic alignmentsequence evolutionstatistical alignmentstochastic expectation maximization algorithm

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Applications of statistics to biology and medical sciences; meta analysis (62P10) General biostatistics (92B15)

Abstract: This article proposes a novel approach to statistical alignment of nucleotide sequences by introducing a context dependent structure on the substitution process in the underlying evolutionary model. We propose to estimate alignments and context dependent mutation rates relying on the observation of two homologous sequences. The procedure is based on a generalized pair-hidden Markov structure, where conditional on the alignment path, the nucleotide sequences follow a Markov distribution. We use a stochastic approximation expectation maximization (saem) algorithm to give accurate estimators of parameters and alignments. We provide results both on simulated data and vertebrate genomes, which are known to have a high mutation rate from CG dinucleotide. In particular, we establish that the method improves the accuracy of the alignment of a human pseudogene and its functional gene.

Recommendations

• An Improved Model for Statistical Alignment
• Parameter Estimation in Pair‐hidden Markov Models
• Algorithm for statistical alignment of two sequences derived from a Poisson sequence length distribution
• Parameter estimation in multiple-hidden i.i.d. models from biological multiple alignment
• An improved algorithm for statistical alignment of sequences related by a star tree

Cited in

(8)

• Duality between the local score of one sequence and constrained hidden Markov model
• Parameter estimation in multiple-hidden i.i.d. models from biological multiple alignment
• Model of context-dependent evolution and corrections for goodness-of-fit statistics in the presence of random zeroes
• An Improved Model for Statistical Alignment
• Parameter Estimation in Pair‐hidden Markov Models
• Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates
• Simultaneous sequence alignment and tree construction using hidden Markov models
• Comparing the performance of a reversible jump Markov chain Monte Carlo algorithm for DNA sequences alignment

This page was built for publication: A context dependent pair hidden Markov model for statistical alignment

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2921246)