Using a VOM model for reconstructing potential coding regions in EST sequences

DOI10.1007/S00180-007-0021-8MaRDI QIDQ2271692zbMATH OpenOpenAlexDBLPWikidataFDO

Authors Armin Shmilovici, Irad Ben-Gal

Publication date 8 August 2009

Published in Computational Statistics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s00180-007-0021-8

zbMATH Keywords

context treesgene annotationsprotein coding DNA recognitionvariable order Markov model

Mathematics Subject Classification ID

Markov processes (60J99) Computational methods for problems pertaining to statistics (62-08) Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40)

Review text

The problem of recognition of protein coding DNA regions in expressed sequence tags is discussed. The authors propose algorithms based on variable order Markov (VOM) models for the distributions of coding and non-coding DNA sequences. In VOM models the order of dependence is not fixed but depends on the context (i.e., on the observed sequence). Results of experiments with real data sets are discussed. It is shown that the models are potentially efficient and robust to sequencing errors.

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Cites work

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Cited in

(10)

• Measuring the efficiency of the intraday Forex market with a universal data compression algorithm
• Codon preference and primary sequence structure in protein-coding regions
• In-phase implies large likelihood for independent codon model: distinguishing coding from non-coding sequences
• A boosting method with asymmetric mislabeling probabilities which depend on covariates
• Gene-finding with the VOM model
• scientific article; zbMATH DE number 700905 (Why is no real title available?)
• scientific article; zbMATH DE number 2204336 (Why is no real title available?)
• Two algorithms based on Markov chains and their application to recognition of protein coding genes in prokaryotic genomes
• Classical and quantum algorithms for constructing text from dictionary problem
• Distributions of pattern statistics in sparse Markov models

Describes a project that uses

Uses Software

• EasyGene
• GlimmerHMM
• TigrScan
• ExonHunter
• ESTScan

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