Taher Leila, Rinner Oliver, Garg Saurabh, Sczyrba Alexander, Morgenstern Burkhard
International Graduate School for Bioinformatics and Genome Research, University of Bielefeld, Postfach 10 01 31, 33501 Bielefeld, Germany.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W305-8. doi: 10.1093/nar/gkh386.
Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By contrast, a new class of comparative methods relies on comparing genomic sequences from evolutionary related organisms to each other. These methods are based on the concept of phylogenetic footprinting: they exploit the fact that functionally important regions in genomic sequences are usually more conserved than non-functional regions. We created a WWW-based software program for homology-based gene prediction at BiBiServ (Bielefeld Bioinformatics Server). Our tool takes pairs of evolutionary related genomic sequences as input data, e.g. from human and mouse. The server runs CHAOS and DIALIGN to create an alignment of the input sequences and subsequently searches for conserved splicing signals and start/stop codons near regions of local sequence conservation. Genes are predicted based on local homology information and splice signals. The server returns predicted genes together with a graphical representation of the underlying alignment. The program is available at http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/.
自动基因预测是计算序列分析中的主要挑战之一。传统的基因寻找方法依赖于从先前已知基因推导出来的统计模型。相比之下，一类新的比较方法则依赖于将进化相关生物的基因组序列相互比较。这些方法基于系统发育足迹的概念：它们利用基因组序列中功能重要区域通常比非功能区域更保守这一事实。我们在BiBiServ（比勒费尔德生物信息学服务器）上创建了一个基于网络的用于基于同源性的基因预测的软件程序。我们的工具将进化相关的基因组序列对作为输入数据，例如来自人类和小鼠的序列。该服务器运行CHAOS和DIALIGN来创建输入序列的比对，随后在局部序列保守区域附近搜索保守的剪接信号和起始/终止密码子。基于局部同源性信息和剪接信号来预测基因。服务器返回预测的基因以及基础比对的图形表示。该程序可在http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/获取。
