Piatnitskiĭ M A, Lisitsa A V, Archakov A I
Biomed Khim. 2009 May-Jun;55(3):230-46.
Review is devoted to computational prediction of functionally related proteins by comparative genomics. Growing possibilities of biotechnology for genome sequencing lead to generation of sequences for millions of genes. However, function of majority of these genes is unknown, and can be determined experimentally only for a few of them. Therefore, accurate and robust methods for in silico prediction (annotation) of gene functions are highly required. We describe here the main techniques of comparative genomics, including the standard method based on transferring functions between homologous sequences and also context-based methods, including phylogenetic profiles and gene-neighbor approaches. Modern methods of comparative genomics allow obtaining correct functional annotations for more than a half of all organism proteins.
综述致力于通过比较基因组学对功能相关蛋白质进行计算预测。生物技术在基因组测序方面不断增长的可能性导致了数百万个基因序列的产生。然而，这些基因中的大多数功能未知，并且只能通过实验确定其中少数基因的功能。因此，迫切需要准确且可靠的计算机预测（注释）基因功能的方法。我们在此描述比较基因组学的主要技术，包括基于同源序列之间功能转移的标准方法以及基于上下文的方法，包括系统发育谱和基因邻接方法。现代比较基因组学方法能够为所有生物体蛋白质的一半以上获得正确的功能注释。
