SSCU：用于分析同义密码子使用的选择性分布的R/Bioconductor软件包
SSCU: an R/Bioconductor package for analyzing selective profile in synonymous codon usage
摘要：
背景同义密码子的选择主要受突变和选择的影响。对于基因组内的大多数基因，突变压力是主要的驱动力，但选择强度可以是强的，并且对于特定的基因或密码子组是显性的。更具体地，翻译效率和准确性的选择强度随着基因的表达水平而增加。已经开发了许多统计方法来评估和量化密码子使用中的选择性概况，包括S指数和Akashi检验，但是还没有开发出包括这些检验并使计算自动化的程序或流水线。结果在本研究中，我们发布了一个R软件包SSCU（selective strength for codon usage，v2.4.0），其中包括密码子使用分析工具。该软件包使用两种方法（比较和相关方法）识别最佳密码子，实现用于检测密码子选择的成熟统计，如S指数，Akashi检验，并估计标准基因组统计，如基因组GC 3，RSCU和Nc。结论该软件包对从事密码子使用分析的研究人员非常有用，因此受到生物研究界的普遍关注。该软件包存放在Bioconductor网站上，目前已被下载超过2000次，并被评为前50%的软件包。
英文摘要：
Background Synonymous codon choice is mainly affected by mutation and selection. For the majority of genes within a genome, mutational pressure is the major driving force, but selective strength can be strong and dominant for specific set of genes or codons. More specifically, the selective strength on translational efficiency and accuracy increases with the gene's expression level. Many statistical approaches have been developed to evaluate and quantify the selective profile in codon usage, including S index and Akashi's test, but no program or pipeline has been developed that includes these tests and automates the calculation. Results In this study, we release an R package SSCU (selective strength for codon usage, v2.4.0), which includes tools for codon usage analyses. The package identifies optimal codons using two approaches (comparative and correlative methods), implements well-established statistics for detecting codon selection, such as S index, Akashi's test, and estimates standard genomic statistics, such as genomic GC3, RSCU and Nc. Conclusions The package is useful for researchers working on the codon usage analysis, and thus has general interest to the biological research community. The package is deposited and curated at the Bioconductor site, and has currently been downloaded for more than 2000 times and ranked as top 50% packages.
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