Journal article

Publication year: 2016

Pages: 283-

Journal: Frontiers in Microbiology

Volume number: 7

ISSN: 1664-302X

eISSN: 1664-302X

Open access status: Gold

DOI Link: https://doi.org/10.3389/fmicb.2016.00283

Publisher: Frontiers Media

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 gamma-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.

Harvard Citation style: Sobetzko, P., Jelonek, L., Strickert, M., Han, W., Goesmann, A. and Waldminghaus, T. (2016) DistAMo: A Web-Based Tool to Characterize DNA-Motif Distribution on Bacterial Chromosomes, Frontiers in Microbiology, 7, p. 283. https://doi.org/10.3389/fmicb.2016.00283

APA Citation style: Sobetzko, P., Jelonek, L., Strickert, M., Han, W., Goesmann, A., & Waldminghaus, T. (2016). DistAMo: A Web-Based Tool to Characterize DNA-Motif Distribution on Bacterial Chromosomes. Frontiers in Microbiology. 7, 283. https://doi.org/10.3389/fmicb.2016.00283