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 treesvariable order Markov modelgene annotationsprotein coding DNA recognition

Mathematics Subject Classification ID

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

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Cites work

• scientific article; zbMATH DE number 2204336 (Why is no real title available?)
• scientific article; zbMATH DE number 2243374 (Why is no real title available?)
• A decision-theoretic generalization of on-line learning and an application to boosting
• A universal data compression system
• A universal prediction lemma and applications to universal data compression and prediction
• Adaptive context trees and text clustering
• Relations between entropy and error probability
• Using a stochastic complexity measure to check the efficient market hypothesis

Cited in

(9)

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

Describes a project that uses

Uses Software

• ESTScan
• ExonHunter
• GlimmerHMM
• TigrScan
• EasyGene

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