Gene teams with relaxed proximity constraint

Sun Kim, Jeong Hyeon Choi, Jiong Yang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

24 Scopus citations


Functionally related genes co-evolve, probably due to the strong selection pressure in evolution. Thus we expect that they are present in multiple genomes. Physical proximity among genes, known as gene team, is a very useful concept to discover functionally related genes in multiple genomes. However, there are also many gene sets that do not preserve physical proximity. 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 constraint. 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. Especially, analysis of gene clusters that belong to B. subtilis and E. coli demonstrated that our model predicted many experimentally verified operons and functionally related clusters. Our program is fast enough to provide a sevice on the web at Users can select any combination of 97 genomes to predict gene teams.

Original languageEnglish (US)
Title of host publicationProceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005
PublisherIEEE Computer Society
Number of pages12
ISBN (Print)0769523447, 9780769523446
StatePublished - 2005
Event2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005 - Stanford, CA, United States
Duration: Aug 8 2005Aug 11 2005

Publication series

NameProceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005


Other2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005
Country/TerritoryUnited States
CityStanford, CA

ASJC Scopus subject areas

  • Engineering(all)
  • Medicine(all)


Dive into the research topics of 'Gene teams with relaxed proximity constraint'. Together they form a unique fingerprint.

Cite this