E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI).
E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI).
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DOI：
10.1186/1471-2105-9-65
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发表时间：
2008-01-29
影响因子：
3
通讯作者：
Garcia-Vallvé S
中科院分区：
文献类型：
--
作者：
Puigbò P;Bravo IG;Garcia-Vallvé S
密码子适应指数(CAI)是对DNA或RNA序列的同义密码子使用偏向的度量。它量化了基因的同义密码子使用和参考集合的同义密码子频率之间的相似性。核苷酸或氨基酸组成中的极值对同义密码子的差异偏好有很大影响。因此，为了正确解释计算机辅助教学并为计算机辅助教学分析提供统计支持，有必要根据序列组成确定计算机辅助教学的期望值的界限。尽管有几个免费提供的程序可以计算给定DNA序列的CAI值，但它们都不能纠正组成偏差，也不能提供CAI值的可信区间。E-CAI服务器可在上获得，它是一个网络应用程序，它通过生成具有与输入相似的G+C和氨基酸含量的随机序列来计算一组查询序列的CAI值。还提供了可执行文件、教程、常见问题(FAQ)部分和几个示例。为了举例说明E-CAI服务器的使用，我们分析了人类线粒体基因的密码子适配，这些基因编码线粒体呼吸链的一个亚单位(不包括那些缺乏原核同源基因的基因)，并在核基因组中编码。假设这些基因从原始线粒体转移到核基因组，然后其密码子的使用得到了改善。E-CAI服务器提供直接阈值，用于辨别CAI中的差异是否在统计上显著，或者它们是否仅仅是由查询序列的G+C组成和/或氨基酸组成中的内部偏差引起的伪像。
The Codon Adaptation Index (CAI) is a measure of the synonymous codon usage bias for a DNA or RNA sequence. It quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Extreme values in the nucleotide or in the amino acid composition have a large impact on differential preference for synonymous codons. It is thence essential to define the limits for the expected value of CAI on the basis of sequence composition in order to properly interpret the CAI and provide statistical support to CAI analyses. Though several freely available programs calculate the CAI for a given DNA sequence, none of them corrects for compositional biases or provides confidence intervals for CAI values. The E-CAI server, available at , is a web-application that calculates an expected value of CAI for a set of query sequences by generating random sequences with G+C and amino acid content similar to those of the input. An executable file, a tutorial, a Frequently Asked Questions (FAQ) section and several examples are also available. To exemplify the use of the E-CAI server, we have analysed the codon adaptation of human mitochondrial genes that codify a subunit of the mitochondrial respiratory chain (excluding those genes that lack a prokaryotic orthologue) and are encoded in the nuclear genome. It is assumed that these genes were transferred from the proto-mitochondrial to the nuclear genome and that its codon usage was then ameliorated. The E-CAI server provides a direct threshold value for discerning whether the differences in CAI are statistically significant or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences.
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影响因子：
3
作者：
Pasamontes A;Garcia-Vallve S
通讯作者：
Garcia-Vallve S
影响因子：
10.7
作者：
Drummond, DA;Raval, A;Wilke, CO
通讯作者：
Wilke, CO
影响因子：
10.7
作者：
Garcia-Vallvé, S;Palau, J;Romeu, A
通讯作者：
Romeu, A
影响因子：
14.9
作者：
Nakamura, Y;Gojobori, T;Ikemura, T
通讯作者：
Ikemura, T
影响因子：
3.9
作者：
Morton, BR
通讯作者：
Morton, BR