ArticleFrontiers in microbiology2016
DistAMo: A Web-Based Tool to Characterize DNA-Motif Distribution on Bacterial Chromosomes.
Article in Frontiers in microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Lineage-associated differences in adenine methylation patterns of mammalian-associatedMicrobiology spectrum · 2026Article
- ThemBio · 2025Article
- Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria.Frontiers in microbiology · 2023Review
- Article
- Impacts ofMicrobial genomics · 2022Article
- Genome-wide methylome analysis of two strains belonging to the hypervirulent Neisseria meningitidis serogroup W ST-11 clonal complex.Scientific reports · 2021Article
- Methyltransferase DnmA is responsible for genome-wide N6-methyladenosine modifications at non-palindromic recognition sites in Bacillus subtilis.Nucleic acids research · 2020Article
- gammaBOriS: Identification and Taxonomic Classification of Origins of Replication in Gammaproteobacteria using Motif-based Machine Learning.Scientific reports · 2020Article
- SMRT Sequencing of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability in Adenines Targeted by Restriction Modification Systems.Frontiers in microbiology · 2020Article
- The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines.Scientific reports · 2018Article
- Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae.PLoS genetics · 2018Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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