Gene-finding with the VOM model

K. O. Shohat-Zaidenraise, A. Shmilovici, I. Ben-Gal

Research output: Contribution to journalArticlepeer-review

Abstract

We present the architecture of an elementary gene-finding algorithm that is based on a Variable Order Markov model (VOM). The VOM model is a generalization of the traditional Markov model that can cope with varying memory dependencies. The VOM model is more efficient in terms of its parameterization and therefore can be trained on relatively short sequences. Experiments with the proposed gene-finder (GF) on three prokaryotic genomes indicate its potential advantage on the detection of short genes.

Original languageEnglish
Pages (from-to)45-54
Number of pages10
JournalJournal of Computational Methods in Sciences and Engineering
Volume7
Issue number1
DOIs
StatePublished - 2007

Keywords

  • Gene finding
  • Variable Order Markov models
  • sequence analysis

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