title: An evaluation of information content as a metric for the inference of putative conserved noncoding regions in DNA sequences using a genetic algorithms approach.
abstract: In previous work, we presented GAMI, an approach to motif inference that uses a genetic algorithms search. GAMI is designed specifically to find putative conserved regulatory motifs in noncoding regions of divergent species, and is designed to allow for analysis of long nucleotide sequences. In this work, we compare GAMI's performance when run with its original fitness function (a simple count of the number of matches) and when run with information content, as well as several variations on these metrics. Results indicate that information content does not identify highly conserved regions, and thus is not the appropriate metric for this task, while variations on information content as well as the original metric succeed in identifying putative conserved regions.
authors.affiliation: Computer Science Department, University of Southern Maine, Portland 04104, USA. congdon@usm.maine.edu
authors.forename: Clare Bates
authors.initials: CB
authors.lastname: Congdon
authors.forename: Joseph C
authors.initials: JC
authors.lastname: Aman
authors.forename: Gerardo M
authors.initials: GM
authors.lastname: Nava
authors.forename: H Rex
authors.initials: HR
authors.lastname: Gaskins
authors.forename: Carolyn J
authors.initials: CJ
authors.lastname: Mattingly
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D016001:Confidence Intervals; D017124:Conserved Sequence / Q000235:genetics*; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000235:genetics; D004742:Enhancer Elements, Genetic / Q000235:genetics; D005982:Glutathione Transferase / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D051876:Sex-Determining Region Y Protein / Q000235:genetics
chemical_list: D019005:Cystic Fibrosis Transmembrane Conductance Regulator; D005982:Glutathione Transferase; D051876:Sex-Determining Region Y Protein