ArticleBMC bioinformatics2005
Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns".
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- The convergent xenogeneic silencer MucR predisposes α-proteobacteria to integrate AT-rich symbiosis genes.Nucleic acids research · 2022Article
- Database of Periodic DNA Regions in Major Genomes.BioMed research international · 2017Article
- Profile-statistical periodicity of DNA coding regions.DNA research : an international journal for rapid publication of reports on genes and genomes · 2011Article
- Bacteria as computers making computers.FEMS microbiology reviews · 2009Review
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. This bias is present throughout a given genome, both in coding and non-coding sequences. Until now this bias remained of unknown origin.
resultsUsing a technique for analysis of auto-correlations based on linear projection, we identified the sequences responsible for the bias. Prokaryotic and lower eukaryotic genomes are covered with ubiquitous patterns that we termed "class A flexible patterns". Each pattern is composed of up to ten conserved nucleotides or dinucleotides distributed into a discontinuous motif. Each occurrence spans a region up to 50 bp in length. They belong to what we named the "flexible pattern" type, in that there is some limited fluctuation in the distances between the nucleotides composing each occurrence of a given pattern. When taken together, these patterns cover up to half of the genome in the majority of prokaryotes. They generate the previously recognized 11 bp periodic bias.
conclusionJudging from the structure of the patterns, we suggest that they may define a dense network of protein interaction sites in chromosomes.
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