初步建立真核基因调控元件模块的搜索方法

南方医科大学学报 ›› 2004, Vol. 24 ›› Issue (02): 172-176.

初步建立真核基因调控元件模块的搜索方法

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

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

出版日期:2004-02-20 发布日期:2004-02-20
基金资助:
收稿日期:2003-9-22。
基金项目: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)
作者简介:钟东(1967-),男,广东梅县人,博士,电话:020-84223814,E-mail:zongjohn@263.net

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

ZHONG Dong¹, ZHANG Zhen-shu¹, LIU Yu-hu¹, ZHENG Guo-qing², LIU Xiao-yi², LU Yang², ZHAO Gui-jun², XU An-long²

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

Online:2004-02-20 Published:2004-02-20

摘要/Abstract

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。

Abstract: 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.

中图分类号:

R318.04

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. 初步建立真核基因调控元件模块的搜索方法[J]. 南方医科大学学报, 2004, 24(02): 172-176.

ZHONG Dong¹, ZHANG Zhen-shu¹, LIU Yu-hu¹, ZHENG Guo-qing², LIU Xiao-yi², LU Yang², ZHAO Gui-jun², XU An-long². Establishment of the methods for searching eukaryotic gene cis-regulatory modules[J]. Journal of Southern Medical University, 2004, 24(02): 172-176.

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