A hybrid gene team model and its application to genome analysis

Sun Kim, Jeong Hyeon Choi, Amit Saple, Jiong Yang

Research output: Contribution to journalArticle

10 Scopus citations

Abstract

It is well-known that functionally related genes occur in a physically clustered form, especially operons in bacteria. By leveraging on this fact, there has recently been an interesting problem formulation known as gene team model, which searches for a set of genes that co-occur in a pair of closely related genomes. However, many gene teams, even experimentally verified operons, frequently scatter within other genomes. Thus, the gene team model should be refined to reflect this observation. In this paper, we generalized the gene team model, that looks for gene clusters in a physically clustered form, to multiple genome cases with relaxed constraints. We propose a novel hybrid pattern model that combines the set and the sequential pattern models. Our model searches for gene clusters with and/or without physical proximity constraint. This model is implemented and tested with 97 genomes (120 replicons). The result was analyzed to show the usefulness of our model. We also compared the result from our hybrid model to those from the traditional gene team model. We also show that predicted gene teams can be used for various genome analysis: operon prediction, phylogenetic analysis of organisms, contextual sequence analysis and genome annotation. Our program is fast enough to provide a service on the web at http://platcom.informatics.indiana.edu/platcom/. Users can select any combination of 97 genomes to predict gene teams.

Original languageEnglish (US)
Pages (from-to)171-196
Number of pages26
JournalJournal of Bioinformatics and Computational Biology
Volume4
Issue number2
DOIs
StatePublished - Apr 1 2006
Externally publishedYes

Keywords

  • Cog team
  • Gene cluster
  • Gene team
  • Hybrid model
  • Proximity constraint

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

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