ArticleThe open microbiology journal2010
Strong Strand Composition Bias in the Genome of Ehrlichia canis Revealed by Multiple Methods.
Article in The open microbiology journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed, 15 citations in OpenAlex.
- Codon Usage Bias and Cluster Analysis of theGenetics research · 2022Article
- Novel metrics for quantifying bacterial genome composition skews.BMC genomics · 2018Article
- Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes.International journal of molecular sciences · 2015Article
- Comparative investigation of the various determinants that influence the codon and amino acid usage patterns in the genus Bifidobacterium.World journal of microbiology & biotechnology · 2015Article
- A Brief Review: The Z-curve Theory and its Application in Genome Analysis.Current genomics · 2014Article
- Microbial lifestyle and genome signatures.Current genomics · 2012Article
- Measures of compositional strand bias related to replication machinery and its applications.Current genomics · 2012Article
- Coding constraints modulate chemically spontaneous mutational replication gradients in mitochondrial genomes.Current genomics · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genes located on the two replicating strands are found to have two separate base/codon usages in Ehrlichia canis genome. Although strand-specific codon usage is not the first observation, for the first time we have applied multiple methods to the analysis of strand composition bias. By combining multiple methods, comprehensive and interesting results are obtained. Among three types of correspondence analysis (COA), absolute codon usages between genes on the two replicating strands are more distinct than relative synonymous codon usage (RSCU) and base usages are more sensitive than both types of codon usages. PR2-plots show that replication-induced bias is much higher than transcription/translation associated bias in the genome. By using the Z curve method, two common genomic characters, i.e., stronger strand composition bias and lower rearrangement frequency are found to exist in 11 obligate intracellular bacteria with separate base/codon usages. We hope more and more researchers will use the multiple methods to analyze strand composition bias in sequenced microbes, particularly obligate intracellular bacteria.
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Registered trials
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.