Fiedler Thomas, Rehmsmeier Marc
Center for Biotechnology, CeBiTec, Universität Bielefeld, 33594 Bielefeld, Germany.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W546-50. doi: 10.1093/nar/gkl250.
Gene regulation is the process through which an organism effects spatial and temporal differences in gene expression levels. Knowledge of cis-regulatory elements as key players in gene regulation is indispensable for the understanding of the latter and of the development of organisms. Here we present the tool jPREdictor for the fast and versatile prediction of cis-regulatory elements on a genome-wide scale. The prediction is based on clusters of individual motifs and any combination of these into multi-motifs with selectable minimal and maximal distances. Individual motifs can be of heterogenous classes, such as simple sequence motifs or position-specific scoring matrices. Cluster scores are weighted occurrences of multi-motifs, where the weights are derived from positive and negative training sets. We illustrate the flexibility of the jPREdictor with a new predic-tion of Polycomb/Trithorax Response Elements in Drosophila melanogaster. jPREdictor is available as a graphical user interface for online use and for download at http://bibiserv.techfak.uni-bielefeld.de/jpredictor.
基因调控是生物体实现基因表达水平在空间和时间上差异的过程。顺式调控元件作为基因调控的关键参与者，对于理解基因调控以及生物体的发育不可或缺。在此，我们展示了工具jPREdictor，用于在全基因组范围内快速且多功能地预测顺式调控元件。该预测基于单个基序的聚类以及这些基序组合成具有可选择最小和最大距离的多基序。单个基序可以属于不同类别，例如简单序列基序或位置特异性评分矩阵。聚类分数是多基序的加权出现次数，其中权重来自正训练集和负训练集。我们通过对黑腹果蝇中多梳/三胸反应元件的新预测来说明jPREdictor的灵活性。jPREdictor以图形用户界面形式提供，可在线使用，也可从http://bibiserv.techfak.uni-bielefeld.de/jpredictor下载。
