P-Match: transcription factor binding site search by combining patterns and weight matrices.
P-Match: transcription factor binding site search by combining patterns and weight matrices.
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DOI：
10.1093/nar/gki441
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发表时间：
2005-07-01
影响因子：
14.9
通讯作者：
Kel AE
中科院分区：
文献类型：
--
作者：
Chekmenev DS;Haid C;Kel AE
p匹配是DNA序列中识别转录因子（TF）结合位点的新工具。 ®数据库。在识别精度上，我们选择了三组优化的截止值，以最大程度地减少虚假否定或假阳性，或与重量矩阵方法（例如Match™工具）相比的总和。较低的假负错误区域（高灵敏度）的卓越识别精度。或用户定义的截止值。
P-Match is a new tool for identifying transcription factor (TF) binding sites in DNA sequences. It combines pattern matching and weight matrix approaches thus providing higher accuracy of recognition than each of the methods alone. P-Match is closely interconnected with the TRANSFAC® database. In particular, P-Match uses the matrix library as well as sets of aligned known TF-binding sites collected in TRANSFAC® and therefore provides the possibility to search for a large variety of different TF binding sites. Using results of extensive tests of recognition accuracy, we selected three sets of optimized cut-off values that minimize either false negatives or false positives, or the sum of both errors. Comparison with the weight matrix approaches such as Match™ tool shows that P-Match generally provides superior recognition accuracy in the area of low false negative errors (high sensitivity). As familiar to the user of Match™, P-Match also allows to save user-specific profiles that include selected subsets of matrices with corresponding TF-binding sites or user-defined cut-off values. Furthermore, a number of tissue-specific profiles are provided that were compiled by the TRANSFAC® team. A public version of the P-Match tool is available at .