Duality between the local score of one sequence and constrained hidden Markov model

DOI10.1007/S11009-021-09856-8MaRDI QIDQ2157385zbMATH OpenOpenAlexFDO

Authors Sabine Mercier, Gregory Nuel

Publication date 28 July 2022

Published in Methodology and Computing in Applied Probability (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s11009-021-09856-8

zbMATH Keywords

HMMposterior distributionmaximum scoring subsequencelocal scorebiological sequence analysisforward/backward

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Bayesian inference (62F15) Markov processes: estimation; hidden Markov models (62M05) Bayesian problems; characterization of Bayes procedures (62C10)

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Cites work

• scientific article; zbMATH DE number 699389 (Why is no real title available?)
• A context dependent pair hidden Markov model for statistical alignment
• An improved approximation for assessing the statistical significance of molecular sequence features
• Approximations for Distributions of Scan Statistics
• Asymptotic behavior of the local score of independent and identically distributed random sequences.
• Biological Sequence Analysis
• Computing posterior probabilities for score-based alignments using ppALIGN
• DNA, words and models. Statistics of exceptional words. Translated from the 2003 French original
• Detecting Local High-Scoring Segments: a First-Stage Approach for Genome-Wide Association Studies
• Distributions associated with general runs and patterns in hidden Markov models
• Elements related to the largest complete excursion of a reflected BM stopped at a fixed time. Application to local score
• Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
• Exact distribution of the local score for Markovian sequences
• Fast estimation of posterior probabilities in change-point analysis through a constrained hidden Markov model
• GENMARK: Parallel gene recognition for both DNA strands
• Improvements on the distribution of maximal segmental scores in a Markovian sequence
• Limit distributions of maximal segmental score among Markov-dependent partial sums
• Maximal length of common words among random letter sequences
• Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.
• Probabilistic graphical models.
• Probability density function of the local score position
• Probability that the maximum of the reflected Brownian motion over a finite interval \([0,t]\) is achieved by its last zero before \(t\).
• Scan statistics
• Scan statistics for detecting a local change in variance for two-dimensional normal data
• Scan statistics for monitoring data modeled by a negative binomial distribution
• Strong limit theorems of empirical distributions for large segmental exceedances of partial sums of Markov variables
• Strong limit theorems of empirical functionals for large exceedances of partial sums of i.i.d. variables
• The Erdős-Rényi strong law for pattern matching with a given proportion of mismatches

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