A suite of web-based programs to search for transcriptional regulatory motifs
A suite of web-based programs to search for transcriptional regulatory motifs
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DOI：
10.1093/nar/gkh461
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Liu, XS
中科院分区：
文献类型：
--
作者：
Liu, YY;Wei, LP;Liu, XS
调控基序的识别对于基因表达的研究具有重要意义。在这里，我们介绍了一套我们开发的用于搜索调控序列基序的程序：(I)BioProspector，一个基于Gibbs抽样的程序，用于从原核生物或低等真核生物的共调控基因中预测调控基序；(Ii)CompareProspector，它是BioProspector的扩展，包含用于高等真核生物的比较基因组学特征；(Iii)MDScan，用于从芯片上的靶标中寻找蛋白质-DNA相互作用位点。这三个程序都检查了一组可能共享共同调控基序的序列，并将假设基序列表输出为特定于位置的概率矩阵、用于构建基序的各个位置以及输入序列上每个位置的位置。可以在http://seqmotifs.stanford.edu.上访问Web服务器和可执行文件
The identification of regulatory motifs is important for the study of gene expression. Here we present a suite of programs that we have developed to search for regulatory sequence motifs: (i) BioProspector, a Gibbs-sampling-based program for predicting regulatory motifs from co-regulated genes in prokaryotes or lower eukaryotes; (ii) CompareProspector, an extension to BioProspector which incorporates comparative genomics features to be used for higher eukaryotes; (iii) MDscan, a program for finding protein-DNA interaction sites from ChIP-on-chip targets. All three programs examine a group of sequences that may share common regulatory motifs and output a list of putative motifs as position-specific probability matrices, the individual sites used to construct the motifs and the location of each site on the input sequences. The web servers and executables can be accessed at http://seqmotifs.stanford.edu.