Inferring the functional relationships among proteins remains a challenging task in the post-genomics. With the increasing number of completed genomes and comparative genomics methods, application of phylogenetic profiles as a predictor of protein function has been proven to be a promising strategy for inferring the relationship of the proteins. This paper reviews important progress made in recent years towards understanding protein function by the application of the phylogenetic profile method. At the same time, some of the major challenges faced by protein function prediction are highlighted. The aim of this review is to emphasize the prospect of comparative genomic strategy that may be used to reach the important objective of protein function prediction. Furthermore, several important informatics resources currently available in this field are summarized. It is believed that these resources and methods can be utilized and integrated with other computational methods to provide valuable insight into elucidating the function of molecular networks.

中文翻译：

---

基于系统发育谱方法的蛋白质功能预测。

在后基因组学中，推断蛋白质之间的功能关系仍然是一项艰巨的任务。随着完整基因组数量的增加和比较基因组学方法的发展，系统发育谱作为蛋白质功能的预测因子的应用已被证明是推断蛋白质关系的一种有前途的策略。本文回顾了近年来通过系统进化分析方法在理解蛋白质功能方面取得的重要进展。同时，突出了蛋白质功能预测面临的一些主要挑战。本文的目的是强调比较基因组策略的前景，该策略可用于实现蛋白质功能预测的重要目标。此外，总结了该领域当前可获得的一些重要信息学资源。相信可以利用这些资源和方法并将其与其他计算方法集成在一起，从而为阐明分子网络的功能提供有价值的见解。