蛋白质家族模体(motif)的评价策略  

A New Strategy to Evaluate Protein Motifs

作　　者：杜春娟[1] 朱云平[2] 贺福初[2] 曾衍钧[1] 

机构地区：[1]北京工业大学生命科学与生物工程学院,北京100022 [2]军事医学科学院北京放射医学研究所,北京100850

出　　处：《北京生物医学工程》2005年第2期97-102,共6页Beijing Biomedical Engineering

基　　金：国家 8 63计划 (2 0 0 2BA711A11;2 0 0 4BA711A2 1)资助 ;国家 973计划 (2 0 0 1CB5 10 2 0 9)资助 ;北京市科技计划项目 (H0 3 0 2 3 0 2 80 5 90 )资助 ;国家自然科学基金项目(创新研究群体科学基金 ) (3 2 10 0 3 )资助

摘　　要：模体是刻画蛋白质家族组成结构和执行功能的重要部分 ,但是对于通过各种生物信息学方法识别出的模体 ,目前没有很好的办法辨别真假和优劣。文中提出一种新的模体评价策略 ,从分类器的观点出发 ,对不同方法在同一个蛋白质家族上建立的不同模体进行比较 ,从而推断出最具有生物意义的模体。本文在PROSITE数据库中选取 7个细胞因子家族 ,采用MEME和HMMER两种模体识别方法分别识别每个家族的模体 ,将每个模体看作一个分类器 ,通过计算同一家族的每个模体的敏感性和特异性并比较它们对应的接收机操作特性曲线 ,进而比较不同模体 ,确定真的模体和排除假的模体 ,从而获得每个蛋白质家族的最佳模体的模型。这种策略可以应用于对任意蛋白质家族模体识别结果的评价。此外 ,还可以利用最佳模体搜索数据库的结果预测每个家族的新成员。Motif is an important concept for describing the common structure and function shared by the members of a protein family. Anyhow, it is still a difficult task to properly identify and evaluate the motifs derived from various bioinformatical means. This paper introduces a new strategy for evaluating motifs, which is based upon the notation of classifier. It compares those motifs constructed by various methods based upon a single protein family, and implies the best motif that of the most biologically significant. Seven cytokine families in the PROSITE protein database are processed by both the MEME and HMMER methods to generate their respective motifs, then each individual motif is regarded as a classifier and used to compute both its sensitivity and specificity indices for the same cytokine family, and the resulting receiver operating characteristic curves derived from their corresponding motifs are compared; these indices and comparisons are used to sort out the best motif model for each cytokine family, meanwhile either true or false motif is discriminated quantitatively. Such a strategy may be expanded further for evaluating any motif for any protein family, and the best motif may be used to predict novel member(s) for a given protein family by means of database searching.

关 键 词：MEME HMMER 接收机操作特性曲线 蛋白质家族模体 细胞因子 模体识别 

分 类 号：Q51[生物学—生物化学]