Abstract

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.