Matlnspector and beyond: promoter analysis based on transcription factor binding sites
Matlnspector and beyond: promoter analysis based on transcription factor binding sites
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DOI：
10.1093/bioinformatics/bti473
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发表时间：
2005-07-01
期刊：
影响因子：
5.8
通讯作者：
Werner, T
中科院分区：
文献类型：
--
作者：
Cartharius, K;Frech, K;Werner, T
动机：启动子分析是识别调控网络的关键一步。成功的启动子分析的前提是以合理的准确性预测潜在的转录因子结合位点。启动子分析的下一步只能通过可靠的预测来进行，例如找到系统发育保守的模式或在共调控基因的启动子中识别更高阶的位点组合。结果：我们提出了一个新版本的MatInspector程序，它使用一个大的权重矩阵库来识别核苷酸序列中的TFBS。通过引入矩阵族的概念、优化的阈值和比较分析，增强的程序产生简洁的结果，避免了冗余和假阳性匹配。我们描述了一些基于MatInspector的程序，允许深入的启动子分析(DiAlignTF，FrameWorker)和调控序列的靶向设计(SequenceShaper)。可用性：MatInspector和这里描述的其他程序可以在http://www.genomatix.de/matinspector.html.上在线使用登记后，在一定的限制范围内免费使用(例如，目前每月分析的次数限制为20次任意序列的分析)。
Motivation: Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes.Results: We present a new version of the program MatInspector that identifies TFBS in nucleoticle sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).Availability: MatInspector and the other programs described here can be used online at http://www.genomatix.de/matinspector.html. Access is free after registration within certain limitations (e.g. the number of analysis per month is currently limited to 20 analyses of arbitrary sequences).