ArticleBMC genomics2003
Wavelet to predict bacterial ori and ter: a tendency towards a physical balance.
Article in BMC genomics, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- gammaBOriS: Identification and Taxonomic Classification of Origins of Replication in Gammaproteobacteria using Motif-based Machine Learning.Scientific reports · 2020Article
- Distinct evolutionary origins of common multi-drug resistance phenotypes in Salmonella typhimurium DT104: a convergent process for adaptation under stress.Molecular genetics and genomics : MGG · 2019Article
- The Divided Bacterial Genome: Structure, Function, and Evolution.Microbiology and molecular biology reviews : MMBR · 2017Review
- Application of discrete wavelet transform for analysis of genomic sequences of Mycobacterium tuberculosis.SpringerPlus · 2016Article
- Examination of prokaryotic multipartite genome evolution through experimental genome reduction.PLoS genetics · 2014Article
- Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: a new appraisal.BMC genomics · 2014Article
- Francisella tularensis Subtype A.II Genomic Plasticity in Comparison with Subtype A.I.PloS one · 2014Article
- The alternative translational profile that underlies the immune-evasive state of persistence in Chlamydiaceae exploits differential tryptophan contents of the protein repertoire.Microbiology and molecular biology reviews : MMBR · 2012Review
- Bacterial phylogenetic tree construction based on genomic translation stop signals.Microbial informatics and experimentation · 2012Article
- Measures of compositional strand bias related to replication machinery and its applications.Current genomics · 2012Article
- CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.PloS one · 2011Article
- Chromosomal rearrangements formed by rrn recombination do not improve replichore balance in host-specific Salmonella enterica serovars.PloS one · 2010Article
- Article
- Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content.BMC genomics · 2009Article
- Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes.BMC genomics · 2007Article
- Quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes.BMC genomics · 2007Article
- The wavelet-based cluster analysis for temporal gene expression data.EURASIP journal on bioinformatics & systems biology · 2007Article
- Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts.Journal of bacteriology · 2006Article
- The genome of Salmonella enterica serovar gallinarum: distinct insertions/deletions and rare rearrangements.Journal of bacteriology · 2005Article
- Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: a tool for identifying differentially regulated genes.Genome research · 2005Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChromosomal DNA replication in bacteria starts at the origin (ori) and the two replicores propagate in opposite directions up to the terminus (ter) region. We hypothesize that the two replicores need to reach ter at the same time to maintain a physical balance; DNA insertion would disrupt such a balance, requiring chromosomal rearrangements to restore the balance. To test this hypothesis, we needed to demonstrate that ori and ter are in a physical balance in bacterial chromosomes. Using wavelet analysis, we documented GC skew, AT skew, purine excess and keto excess on the published bacterial genomic sequences to locate the turning (minimum and maximum) points on the curves. Previously, the minimum point had been supposed to correlate with ori and the maximum to correlate with ter.
resultsWe observed a strong tendency of the bacterial chromosomes towards a physical balance, with the minima and maxima corresponding to the known or putative ori and ter and being about half chromosome separated in most of the bacteria studied. A nonparametric method based on wavelet transformation was employed to perform significance tests for the predicted loci.
conclusionsThe wavelet approach can reliably predict the ori and ter regions and the bacterial chromosomes have a strong tendency towards a physical balance between ori and ter.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.