title: AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes.
abstract: BACKGROUND
  Genomes contain biologically significant information that extends beyond that encoded in genes. Some of this information relates to various short dispersed repeats distributed throughout the genome. The goal of this work was to combine tools for detection of statistically significant dispersed repeats in DNA sequences with tools to aid development of hypotheses regarding their possible physiological functions in an easy-to-use web-based environment.
  
  
  RESULTS
  Ab Initio Motif Identification Environment (AIMIE) was designed to facilitate investigations of dispersed sequence motifs in prokaryotic genomes. We used AIMIE to analyze the Escherichia coli and Haemophilus influenzae genomes in order to demonstrate the utility of the new environment. AIMIE detected repeated extragenic palindrome (REP) elements, CRISPR repeats, uptake signal sequences, intergenic dyad sequences and several other over-represented sequence motifs. Distributional patterns of these motifs were analyzed using the tools included in AIMIE.
  
  
  BACKGROUND
  AIMIE and the related software can be accessed at our web site http://www.cmbl.uga.edu/software.html.
authors.affiliation: Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA. mrazek@uga.edu
authors.forename: Jan
authors.initials: J
authors.lastname: Mrázek
authors.forename: Shaohua
authors.initials: S
authors.lastname: Xie
authors.forename: Xiangxue
authors.initials: X
authors.lastname: Guo
authors.forename: Anuj
authors.initials: A
authors.lastname: Srivastava
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics*; D006801:Humans; D020407:Internet; D008969:Molecular Sequence Data; D011387:Prokaryotic Cells / Q000502:physiology*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software