[1]钟东,张振书,刘宇虎,等.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,(02):172-176.
 ZHONG Dong,ZHANG Zhen-shu,LIU Yu-hu,et al.Establishment of the methods for searching eukaryotic gene cis-regulatory modules[J].Journal of Southern Medical University,2004,(02):172-176.
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初步建立真核基因调控元件模块的搜索方法()
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《南方医科大学学报》[ISSN:1673-4254/CN:44-1627/R]

卷:
期数:
2004年02期
页码:
172-176
栏目:
出版日期:
2004-02-01

文章信息/Info

Title:
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
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
Author(s):
ZHONG Dong1 ZHANG Zhen-shu1 LIU Yu-hu1 ZHENG Guo-qing2 LIU Xiao-yi2 LU Yang2 ZHAO Gui-jun2 XU An-long2
1. Department of Gastroenterology, Nanfang Hospital, First Military Medical University, Guangzhou 510515, China;
2. Department of Biochemistry, Sun Yat-sen University, Guangzhou 510275, China
关键词:
真核基因调控元件模块生物信息学
Keywords:
eukaryotic genecis-regulatory modulesbioinformatics
分类号:
R318.04
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.

参考文献/References:

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备注/Memo

备注/Memo:
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
更新日期/Last Update: 1900-01-01