ArticleBMC bioinformatics2012
CBDB: the codon bias database.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- M1CR0B1AL1Z3R 2.0: an enhanced web server for comparative analysis of bacterial genomes at scale.Nucleic acids research · 2025Article
- The Codon Statistics Database: A Database of Codon Usage Bias.Molecular biology and evolution · 2022Article
- CompoDynamics: a comprehensive database for characterizing sequence composition dynamics.Nucleic acids research · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- The Dynamic Codon Biaser: calculating prokaryotic codon usage biases.Microbial genomics · 2021Article
- Codon-based indices for modeling gene expression and transcript evolution.Computational and structural biotechnology journal · 2021Review
- CUBAP: an interactive web portal for analyzing codon usage biases across populations.Nucleic acids research · 2020Article
- Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli.Nature biotechnology · 2018Article
- The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host.Scientific reports · 2018Article
- Article
- A new and updated resource for codon usage tables.BMC bioinformatics · 2017Article
- ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias.Microbial genomics · 2016Article
- Spontaneous phenotypic suppression of GacA-defective Vibrio fischeri is achieved via mutation of csrA and ihfA.BMC microbiology · 2015Article
- Differential codon adaptation between dsDNA and ssDNA phages in Escherichia coli.Molecular biology and evolution · 2014Article
- A comprehensive, high-resolution map of a gene's fitness landscape.Molecular biology and evolution · 2014Article
- tRNA gene copy number variation in humans.Gene · 2014Article
- Vaccinia and influenza A viruses select rather than adjust tRNAs to optimize translation.Nucleic acids research · 2013Article
- Practical tips for construction of custom Peptide libraries and affinity selection by using commercially available phage display cloning systems.Journal of nucleic acids · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed codon usage to translational selection, mutational bias and drift. Furthermore, correlations between codon usage within host genomes and their viral pathogens have been observed for a myriad of host-virus systems. As such, numerous studies have investigated codon usage and codon bias in an effort to better understand how species evolve. Numerous metrics have been developed to identify biases in codon usage. In addition, a few data repositories of codon bias data are available, differing in the metrics reported as well as the number and taxonomy of strains examined. DESCRIPTION: We have created a new web resource called the Codon Bias Database (CBDB) which provides information regarding the codon bias within the set of highly expressed genes for 300+ bacterial genomes. CBDB was developed to provide a resource for researchers investigating codon bias in bacteria, facilitating comparisons between strains and species. Furthermore, the site was created to serve those studying adaptation in phage; the genera selected for this first release of CBDB all have sequenced, annotated bacteriophages. The annotations and sequences for the highly expressed gene set are available for each strain in addition to the strain's codon bias measurements.
conclusionsComparing species and strains provides a comprehensive look at how codon usage has been shaped over evolutionary time and can elucidate the putative mechanisms behind it. The Codon Bias Database provides a centralized repository of look-up tables and codon usage bias measures for a wide variety of genera, species and strains. Through our analysis of the variation in codon usage within the strains presently available, we find that most members of a genus have a codon composition most similar to other members of its genus, although not necessarily other members of its species.
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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.