生物体内硒蛋白的计算机识别方法  

A novel method developed for in silico identification of selenoproteins in vivo

作　　者：刘琼[1] 陈平[2] 姜亮[2] 高中洪[2] 徐辉碧[2] 

机构地区：[1]深圳大学生命科学学院,广东深圳518060 [2]华中科技大学化学系,湖北武汉430074

出　　处：《计算机与应用化学》2006年第8期715-719,共5页Computers and Applied Chemistry

基　　金：国家自然科学基金(30370352;30570420)

摘　　要：硒是人体必需的微量元素,在人体内主要形成硒蛋白。硒蛋白的计算机识别,不仅能预测生物体中硒的形态,而且可为硒的生化性质研究提供理论基础,以阐明硒的生物功能。本文以斑马鱼为研究对象,结合已有生物分析软件,采用PERL语言编程,建立了计算机识别硒蛋白的新方法。它根据硒蛋白基因的判断标准、以目前公布的不同物种的基因组注释信息为基础,将以TGA码终止的基因的再分析、3′-UTR区域中硒代半胱氨酸插入序列(SECIS)结构的检索、同源相似基因中硒代半胱氨酸/半胱氨酸的比对,以及硒蛋白基因编码区的识别等步骤,从已注释的基因组中用计算机寻找和鉴定硒蛋白的形态。当前,已有一些识别硒蛋白的方法,但只能识别专一物种,而本文提出的方法,克服了该缺陷,而且对计算机运算速度和容量无苛刻要求,尤其是发现不同物种新硒蛋白方面有优势。本方法普遍适用于不同物种基因组中,硒蛋白的计算机预测与识别。Selenium is an essential trace element that presents mainly as selenoproteins in vivo. Identification of selenoproteins in silico not only analyzes the speciation of selenium, but also provides theoretical bases for the study of its biochemical properties. It also conduces to the understanding of selenium on its biological effects. Using zebra fish as an object and general bio-software as an assistant, the present study set up a new method to in silico identify selenoproteins by editing a series of programs with PERL language. This method adopted all criterions required for the judgement of selenoprotein genes. Genes used in this study have been predicted from their genome and annotated in the genebank before they were released to the public. Procedures for the speciation analyses were performed stepwise by the extraction of genes ended up with TGA codons, searches for selenocysteine insertion sequence （SECIS） elements in the 3＇- untranslated regions, homogenous alignments for the pair of selenocysteine/cysteine, and recognization of new open reading frames of the candidate selenoprotein genes. The study not only overtops the limitation of ＂ one method for one species＂ in the already used method, but also disclaims requirements for supercomputers in data handling and algorithmic operation. It specifically possesses preponderance in predicting new selenoproteins from their genomes, which can be widely used in all species after the accomplishment of their genomic sequencing and gene annotation.

关 键 词：硒:硒蛋白 硒代半胱氨酸 硒代半胱氨酸插入元件(SECIS) 

分 类 号：Q524[生物学—生物化学]