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CBDB: The codon bias database
BMC Bioinformatics
  • Adam Hilterbrand
  • Joseph Saelens
  • Catherine Putonti, Loyola University Chicago
Document Type
Article
Publication Date
1-1-2012
Disciplines
Abstract
Background In 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. Conclusions Comparing 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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Author Posting. © Hilterbrand et al., 2012. This article is posted here by permission of the authors for personal use, not for redistribution. The article was published in BMC Bioinformatics, Volume 13, Issue 62, 2012, http://dx.doi.org/10.1186/1471-2105-13-62

Creative Commons License
Creative Commons Attribution-Noncommercial-No Derivative Works 3.0
Citation Information
Hilterbrand, A, J Saelens, and C Putonti. "CBDB: The codon bias database." BMC Bioinformatics 13(62), 2012.