初步建立真核基因调控元件模块的搜索方法  

Establishment of the methods for searching eukaryotic gene cis-regulatory modules

作　　者：钟东[1] 张振书[1] 刘宇虎[1] 郑国清[2] 刘小意[2] 卢阳[2] 赵贵军[2] 徐安龙[2] 

机构地区：[1]第一军医大学南方医院消化科,广东广州510515 [2]中山大学生命科学学院生物化学系,广东广州510275

出　　处：《第一军医大学学报》2004年第2期172-176,共5页Journal of First Military Medical University

基　　金：国家自然科学基金重点项目(69935020);国家自然科学基金(30171053);中山大学青年教师科研启动基金(33110-1131091)~~

摘　　要：依据基因调控知识对现有方法进行了综合及改进:(1)在序列搜索方面,结合多序列低分值查询与多个保守片段搜索两种方法获得匹配序列,然后序列相互打分,最后进行聚类分析;(2)在位点搜索方面,综合应用位置权重矩阵、成对寡核苷酸及Smith-Waterman等方法;(3)在分析系统方面,采用面向对象的程序设计方法建立跨平台、可扩展、基于数据库的分析系统。本方法对MHC基因家族的初步分析结果表明,能较准确地找到一些基因调控元件模块所在的区域。On the basis of the knowledge of eukaryotic gene regulation, we modified the method in three aspects: (1) Sear- ching the cis-regulatory modules (CRM) according Fasta or Blast sequence with multiple sequence and low E value, followed by mutual scoring of these sequence with Smith-Waterman algorithms and finally by clustering analysis; (2) Searching the trans- cription factor-binding site using International Union of Pure and Applied Chemistry, Position-Weight Matrix(PWM) and Dyed method; (3) Designing and implementation of data analysis based on the software in Windows 2000 and UNIX using object-oriented technology. The results of analysis of the major histocompatibility complex gene family show that this procedure may accurately locate the regions that contain some of the CRMs.

关 键 词：真核基因 基因调控 搜索方法 调控元件模块 数据库 

分 类 号：TP399[自动化与计算机技术—计算机应用技术]