Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Taiwan.
Brief Funct Genomics. 2012 Jul;11(4):291-9. doi: 10.1093/bfgp/els024. Epub 2012 Jun 28.
Accurate prediction of operons can improve the functional annotation and application of genes within operons in prokaryotes. Here, we review several features: (i) intergenic distance, (ii) metabolic pathways, (iii) homologous genes, (iv) promoters and terminators, (v) gene order conservation, (vi) microarray, (vii) clusters of orthologous groups, (viii) gene length ratio, (ix) phylogenetic profiles, (x) operon length/size and (xi) STRING database scores, as well as some other features, which have been applied in recent operon prediction methods in prokaryotes in the literature. Based on a comparison of the prediction performances of these features, we conclude that other, as yet undiscovered features, or feature selection with a receiver operating characteristic analysis before algorithm processing can improve operon prediction in prokaryotes.
准确预测操纵子可以提高原核生物中操纵子内基因的功能注释和应用。在这里，我们回顾了几种特征：（i）基因间距离，（ii）代谢途径，（iii）同源基因，（iv）启动子和终止子，（v）基因顺序保守性，（vi）基因芯片，（vii）直系同源群聚类，（viii）基因长度比，（ix）系统发育分布，（x）操纵子长度/大小和（xi）STRING 数据库评分，以及一些其他特征，这些特征已经在文献中应用于原核生物的最近的操纵子预测方法。通过比较这些特征的预测性能，我们得出结论，其他尚未发现的特征，或在算法处理前进行基于接收者操作特征分析的特征选择，可以提高原核生物的操纵子预测。
