Genome analysis AIMIE: A Web-based Environment for Detection and Interpretation of Significant Sequence Motifs in Prokaryotic Genomes

Motivation: Genomes contain biologically significant information that extends beyond that encoded in genes. Some of this informa-tion relates to various short dispersed repeats distributed throughout the genome. The goal of this work was to combine tools for detec-tion 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 de-signed 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 REP elements, CRISPR repeats, uptake signal sequences, intergenic dyad se-quences, and several other overrepresented sequence motifs. Dis-tributional patterns of these motifs were analyzed using the tools included in AIMIE. Availability: AIMIE and the related software can be accessed at our web sit