Codon adaptation index as a measure of dominating codon bias
Codon adaptation index as a measure of dominating codon bias
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DOI：
10.1093/bioinformatics/btg272
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发表时间：
2003-11-01
期刊：
影响因子：
5.8
通讯作者：
Képès, F
中科院分区：
文献类型：
--
作者：
Carbone, A;Zinovyev, A;Képès, F
我们提出了一个简单的算法来检测基因组中占主导地位的同义密码子使用偏差。该算法基于对该问题的精确数学表述，从而使我们使用密码子适应指数(CAI)作为密码子偏向的“通用”衡量标准。这一衡量标准以前曾被用于翻译偏见的特定背景下。以这组编码序列作为生物信息的唯一来源，该算法提供了高度代表偏见的参考基因集。这个集合可以用来计算原核生物和真核生物的基因的计算机辅助指数，包括那些功能注释尚未获得的生物。一个重要的应用涉及检测表征翻译偏差的参考集，该参考集已知与表达水平相关；在这种情况下，该算法成为预测基因表达水平、指导调节电路重构和物种比较的关键工具。该算法还可以检测领先-滞后链偏差、GC含量偏差、GC3偏差和水平基因转移。该方法在12种生长缓慢和快速生长的细菌上得到了验证，这些细菌包括酿酒酵母、秀丽线虫和黑腹果蝇。
We propose a simple algorithm to detect dominating synonymous codon usage bias in genomes. The algorithm is based on a precise mathematical formulation of the problem that lead us to use the Codon Adaptation Index (CAI) as a 'universal' measure of codon bias. This measure has been previously employed in the specific context of translational bias. With the set of coding sequences as a sole source of biological information, the algorithm provides a reference set of genes which is highly representative of the bias. This set can be used to compute the CAI of genes of prokaryotic and eukaryotic organisms, including those whose functional annotation is not yet available. An important application concerns the detection of a reference set characterizing translational bias which is known to correlate to expression levels; in this case, the algorithm becomes a key tool to predict gene expression levels, to guide regulatory circuit reconstruction, and to compare species. The algorithm detects also leading-lagging strands bias, GC-content bias, GC3 bias, and horizontal gene transfer. The approach is validated on 12 slow-growing and fast-growing bacteria, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster.