使用CORG工作台对脊椎动物基因组进行比较启动子分析。

Comparative promoter analysis in vertebrate genomes with the CORG workbench.

作者信息

Dieterich Christoph, Vingron Martin

机构信息

Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Berlin, Germany.

出版信息

Methods Mol Biol. 2006;338:105-18. doi: 10.1385/1-59745-097-9:105.

DOI:10.1385/1-59745-097-9:105

PMID:16888353

Abstract

CORG is a versatile web-based workbench for comparative promoter analysis in vertebrate model organisms. Two kinds of information are explicitly considered in the automated annotation process. First, local conservation patterns in upstream regions of homologous genes: These phylogenetic footprints are likely to stem from sequence elements that are under selective pressure. The CORG pipeline detects and exploits patterns of local similarity to annotate promoter regions. Second, experimental data on transcription start sites: exon positions and DNA binding site descriptions complete the promoter annotation. These data are made available via an interactive web portal. Individual promoter studies are supported by a JAVA applet that supplies all data down to the nucleotide level.

摘要

CORG是一个基于网络的多功能工作平台，用于脊椎动物模式生物中的比较启动子分析。在自动注释过程中明确考虑了两种信息。第一，同源基因上游区域的局部保守模式：这些系统发育足迹可能源于处于选择压力下的序列元件。CORG管道检测并利用局部相似性模式来注释启动子区域。第二，转录起始位点的实验数据：外显子位置和DNA结合位点描述完善了启动子注释。这些数据可通过交互式网络门户获取。单个启动子研究由一个JAVA小程序提供支持，该小程序提供直至核苷酸水平的所有数据。