Wittkop Tobias, Rahmann Sven, Baumbach Jan
Genome Informatics, Bielefeld University, Bielefeld, Germany.
J Integr Bioinform. 2010 Mar 25;7(3):461. doi: 10.2390/biecoll-jib-2010-117.
We investigated the problem of imprecisely determined prokaryotic transcription factor (TF) binding sites (TFBSs). We found that the identification and reinvestigation of questionable binding motifs may result in improved models of these motifs. Subsequent modelbased predictions of gene regulatory interactions may be performed with increased accuracy when the TFBSs annotation underlying these models has been re-adjusted. We present MoRAine 2.0, a significantly improved version of MoRAine. It can automatically identify cases of unfavorable TFBS strand annotations and imprecisely determined TFBS positions. With release 2.0, we close the gap between reasonable running time and high accuracy. Furthermore, it requires only minimal input from the user: (1) the input TFBS sequences and (2) the length of the flanking sequences.
MoRAine 2.0 is an easy-to-use, integrated, and publicly available web tool for the re-annotation of questionable TFBSs. It can be used online or downloaded as a stand-alone version from http://moraine.cebitec.uni-bielefeld.de.
我们研究了原核生物转录因子（TF）结合位点（TFBS）确定不准确的问题。我们发现，对有问题的结合基序进行识别和重新研究可能会改进这些基序的模型。当基于这些模型的TFBS注释经过重新调整后，随后基于模型的基因调控相互作用预测可能会更准确地进行。我们展示了MoRAine 2.0，它是MoRAine的一个显著改进版本。它可以自动识别TFBS链注释不利和TFBS位置确定不准确的情况。随着2.0版本的发布，我们缩小了合理运行时间与高精度之间的差距。此外，它只需要用户提供最少的输入：（1）输入的TFBS序列和（2）侧翼序列的长度。
MoRAine 2.0是一个易于使用、集成且公开可用的网络工具，用于对有问题的TFBS进行重新注释。它可以在线使用，也可以从http://moraine.cebitec.uni-bielefeld.de下载独立版本。
