Puigbò Pere, Bravo Ignacio G, Garcia-Vallve Santiago
Department of Biochemistry and Biotechnology, Rovira i Virgili University (URV), Campus Sescelades, c/Marcelli Domingo s/n, 43007 Tarragona, Spain.
Biol Direct. 2008 Sep 16;3:38. doi: 10.1186/1745-6150-3-38.
The Codon Adaptation Index (CAI) was first developed to measure the synonymous codon usage bias for a DNA or RNA sequence. The CAI quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set.
We describe here CAIcal, a web-server available at http://genomes.urv.es/CAIcal that includes a complete set of utilities related with the CAI. The server provides useful important features, such as the calculation and graphical representation of the CAI along either an individual sequence or a protein multiple sequence alignment translated to DNA. The automated calculation of CAI and its expected value is also included as one of the CAIcal tools. The software is also free to be downloaded as a stand alone application for local use.
The CAIcal server provides a complete set of tools to assess codon usage adaptation and to help in genome annotation.
密码子适应指数（CAI）最初是为测量DNA或RNA序列的同义密码子使用偏好而开发的。CAI量化了基因的同义密码子使用与参考集的同义密码子频率之间的相似性。
我们在此介绍CAIcal，这是一个可在http://genomes.urv.es/CAIcal上访问的网络服务器，它包含了一套与CAI相关的实用工具。该服务器提供了一些有用的重要功能，例如沿单个序列或翻译成DNA的蛋白质多序列比对计算CAI并进行图形表示。CAI及其期望值的自动计算也作为CAIcal工具之一包含在内。该软件也可作为独立应用程序免费下载以供本地使用。
CAIcal服务器提供了一套完整的工具来评估密码子使用适应性并有助于基因组注释。
