DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomes
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 quan...
Main Authors: | , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2016-03-01
|
Series: | Frontiers in Microbiology |
Subjects: | |
Online Access: | http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00283/full |
id |
doaj-0ac73b41fb2b42f98346334c7c23d5e9 |
---|---|
record_format |
Article |
spelling |
doaj-0ac73b41fb2b42f98346334c7c23d5e92020-11-24T22:31:52ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2016-03-01710.3389/fmicb.2016.00283181675DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomesPatrick eSobetzko0Lukas eJelonek1Marc eStrickert2Wenxia eHan3Alexander eGoesmann4Torsten eWaldminghaus5LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-University MarburgJustus-Liebig-UniversityLOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-University MarburgLOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-University MarburgJustus-Liebig-UniversityLOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-University MarburgShort 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.http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00283/fullBacteriaComputational BiologyDNA ReplicationEscherichia colibioinformaticsalgorithm |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Patrick eSobetzko Lukas eJelonek Marc eStrickert Wenxia eHan Alexander eGoesmann Torsten eWaldminghaus |
spellingShingle |
Patrick eSobetzko Lukas eJelonek Marc eStrickert Wenxia eHan Alexander eGoesmann Torsten eWaldminghaus DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomes Frontiers in Microbiology Bacteria Computational Biology DNA Replication Escherichia coli bioinformatics algorithm |
author_facet |
Patrick eSobetzko Lukas eJelonek Marc eStrickert Wenxia eHan Alexander eGoesmann Torsten eWaldminghaus |
author_sort |
Patrick eSobetzko |
title |
DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomes |
title_short |
DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomes |
title_full |
DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomes |
title_fullStr |
DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomes |
title_full_unstemmed |
DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomes |
title_sort |
distamo: a web-based tool to characterize dna-motif distribution on bacterial chromosomes |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2016-03-01 |
description |
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. |
topic |
Bacteria Computational Biology DNA Replication Escherichia coli bioinformatics algorithm |
url |
http://journal.frontiersin.org/Journal/10.3389/fmicb.2016.00283/full |
work_keys_str_mv |
AT patrickesobetzko distamoawebbasedtooltocharacterizednamotifdistributiononbacterialchromosomes AT lukasejelonek distamoawebbasedtooltocharacterizednamotifdistributiononbacterialchromosomes AT marcestrickert distamoawebbasedtooltocharacterizednamotifdistributiononbacterialchromosomes AT wenxiaehan distamoawebbasedtooltocharacterizednamotifdistributiononbacterialchromosomes AT alexanderegoesmann distamoawebbasedtooltocharacterizednamotifdistributiononbacterialchromosomes AT torstenewaldminghaus distamoawebbasedtooltocharacterizednamotifdistributiononbacterialchromosomes |
_version_ |
1725735892004372480 |