GENMARK: Parallel gene recognition for both DNA strands

DOI10.1016/0097-8485(93)85004-VMaRDI QIDQ4326274zbMATH OpenWikidataFDO

Authors Mark Borodovsky, James McIninch

Publication date 14 May 1995

Published in Computers & Chemistry (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/0097-8485(93)85004-V

zbMATH Keywords

Bayesian algorithmDNA strandslarge-scale DNA sequencingnon-homogeneous Markov chain modelpredicting gene locationsprotein-coding regions

Mathematics Subject Classification ID

Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20)

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• Classifying molecular sequences using a linkage graph with their pairwise similarities
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• A Markovian approach for the prediction of mouse isochores
• An unusual 500,000 bases long oscillation of guanine and cytosine content in human chromosome 21
• Construction of a mathematical model of DNA in the form of a uniform Markov chain and perspectives of its application to gene recognition
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• Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains
• Fitting DNA sequences through log-linear modelling with linear constraints
• On the prediction of genes based on the asymptotic local approach
• scientific article; zbMATH DE number 3896722 (Why is no real title available?)
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• Using compositions of Markov models to determine functional gene fragments
• Two algorithms based on Markov chains and their application to recognition of protein coding genes in prokaryotic genomes
• Effective hidden Markov models for detecting splicing junction sites in DNA sequences
• Uniform accuracy of the maximum likelihood estimates for probabilistic models of biological sequences
• Scalable test of statistical significance for protein-DNA binding changes with insertion and deletion of bases in the genome

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