title: DistAMo: A Web-Based Tool to Characterize DNA-Motif Distribution on Bacterial Chromosomes.
abstract: Short DNA motifs are involved in a multitude of functions such as for example chromosome segregation, DNA replication or mismatch repair. Distribution of such motifs is often not random and the specific chromosomal pattern relates to the respective motif function. Computational approaches which quantitatively assess such chromosomal motif patterns are necessary. Here we present a new computer tool DistAMo (Distribution Analysis of DNA Motifs). The algorithm uses codon redundancy to calculate the relative abundance of short DNA motifs from single genes to entire chromosomes. Comparative genomics analyses of the GATC-motif distribution in γ-proteobacterial genomes using DistAMo revealed that (i) genes beside the replication origin are enriched in GATCs, (ii) genome-wide GATC distribution follows a distinct pattern, and (iii) genes involved in DNA replication and repair are enriched in GATCs. These features are specific for bacterial chromosomes encoding a Dam methyltransferase. The new software is available as a stand-alone or as an easy-to-use web-based server version at http://www.computational.bio.uni-giessen.de/distamo.
authors.affiliation: Chromosome Biology Group, LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-University Marburg Marburg, Germany.
authors.forename: Patrick
authors.initials: P
authors.lastname: Sobetzko
authors.affiliation: Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University Giessen, Germany.
authors.forename: Lukas
authors.initials: L
authors.lastname: Jelonek
authors.affiliation: Chromosome Biology Group, LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-University Marburg Marburg, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Strickert
authors.affiliation: Chromosome Biology Group, LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-University Marburg Marburg, Germany.
authors.forename: Wenxia
authors.initials: W
authors.lastname: Han
authors.affiliation: Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University Giessen, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.affiliation: Chromosome Biology Group, LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-University Marburg Marburg, Germany.
authors.forename: Torsten
authors.initials: T
authors.lastname: Waldminghaus
keywords: DNA replication; Escherichia coli; algorithm; bacteria; bioinformatics; chromosome maintenance; computational biology