CBDB: the codon bias database.
CBDB: the codon bias database.
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DOI：
10.1186/1471-2105-13-62
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发表时间：
2012-04-26
影响因子：
3
通讯作者：
Putonti C
中科院分区：
文献类型：
--
作者：
Hilterbrand A;Saelens J;Putonti C
在许多基因组中，存在使用特定密码子的明显偏好。诱导密码子偏好的机制仍然是一个悬而未决的问题;研究将密码子使用归因于翻译选择、突变偏好和漂移。此外，宿主基因组内的密码子使用和它们的病毒病原体之间的相关性已经在无数宿主-病毒系统中观察到。因此，许多研究调查了密码子使用和密码子偏好，以更好地了解物种如何进化。已经开发了许多度量来鉴定密码子使用中的偏差。此外，一些密码子偏好数据的数据库是可用的，在报告的度量以及所检查的菌株的数量和分类方面有所不同。我们已经创建了一个新的网络资源，称为密码子偏好数据库（CBDB），它提供了关于300多个细菌基因组的高表达基因组内的密码子偏好的信息。CBDB的开发是为了为研究细菌密码子偏好的研究人员提供资源，促进菌株和物种之间的比较。此外，该网站的创建是为了服务于那些研究噬菌体适应性的人;为CBDB的第一个版本选择的属都有测序，注释的噬菌体。除了菌株的密码子偏好测量之外，还可获得每个菌株的高表达基因集的注释和序列。比较物种和菌株提供了一个全面的了解如何密码子的使用已形成在进化的时间，并可以阐明其背后的假定机制。密码子偏差数据库提供了一个集中的存储库的查找表和密码子的使用偏置措施，为各种各样的属，种和菌株。通过我们对目前可用的菌株内密码子使用的变化的分析，我们发现一个属的大多数成员具有与其属的其他成员最相似的密码子组成，尽管不一定是其物种的其他成员。
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. 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. 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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DOI：
10.1093/dnares/5.6.319
发表时间：
1998-12-31
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Kunisawa, T;Kanaya, S;Kutter, E
通讯作者：
Kutter, E
影响因子：
3.5
作者：
Kanaya, S;Yamada, Y;Ikemura, T
通讯作者：
Ikemura, T
影响因子：
3.7
作者：
Clarke TF 4th;Clark PL
通讯作者：
Clark PL
影响因子：
6.7
作者：
Greenbaum BD;Levine AJ;Bhanot G;Rabadan R
通讯作者：
Rabadan R
影响因子：
14.9
作者：
Angellotti MC;Bhuiyan SB;Chen G;Wan XF
通讯作者：
Wan XF