Preliminary results for GAMI: A genetic algorithms approach to motif inference

Clare Bates Congdon, Charles W. Fizer, Noah W. Smith, H Rex Gaskins, Joseph Aman, Gerardo M. Nava, Carolyn Mattingly

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

Abstract

We have developed GAMI, an approach to motif inference that uses a genetic algorithms search and is designed specifically to work with divergent species and possibly long nucleotide sequences. The system design reduces the size of the search space as compared to typical window-location approaches for motif inference. This paper describes the motivation and system design for GAMI, discusses how we have designed the search space and compares this to the search space of other approaches, and presents initial results with data from the literature and from novel tasks. GAMI is able to find a host of putative conserved patterns; possible approaches for validating the utility of the conserved regions are discussed.

Original languageEnglish (US)
Title of host publicationProceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05
StatePublished - Dec 1 2005
Event2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05 - La Jolla, CA, United States
Duration: Nov 14 2005Nov 15 2005

Publication series

NameProceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05
Volume2005

Other

Other2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05
CountryUnited States
CityLa Jolla, CA
Period11/14/0511/15/05

ASJC Scopus subject areas

  • Engineering(all)

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  • Cite this

    Congdon, C. B., Fizer, C. W., Smith, N. W., Gaskins, H. R., Aman, J., Nava, G. M., & Mattingly, C. (2005). Preliminary results for GAMI: A genetic algorithms approach to motif inference. In Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05 [1594904] (Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05; Vol. 2005).