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

Journal of Southern Medical University ›› 2004, Vol. 24 ›› Issue (02): 172-176.

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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

Abstract

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.

CLC Number:

R318.04

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

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