一套用于搜索转录调控基序的基于网络的程序。
A suite of web-based programs to search for transcriptional regulatory motifs.
作者信息
Liu Yueyi, Wei Liping, Batzoglou Serafim, Brutlag Douglas L, Liu Jun S, Liu X Shirley
机构信息
Stanford Medical Informatics, 251 Campus Drive X215, Stanford, CA 94305, USA.
出版信息
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W204-7. doi: 10.1093/nar/gkh461.
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.
调控基序的识别对于基因表达研究至关重要。在此，我们展示了我们开发的一套用于搜索调控序列基序的程序：（i）BioProspector，一个基于吉布斯采样的程序，用于从原核生物或低等真核生物中共同调控的基因预测调控基序；（ii）CompareProspector，BioProspector的扩展，它整合了比较基因组学特征，用于高等真核生物；（iii）MDscan，一个用于从芯片上染色质免疫沉淀（ChIP-on-chip）靶点中寻找蛋白质-DNA相互作用位点的程序。所有这三个程序都检查一组可能共享共同调控基序的序列，并输出一份假定基序列表，作为位置特异性概率矩阵、用于构建基序的各个位点以及每个位点在输入序列上的位置。可通过http://seqmotifs.stanford.edu访问网络服务器和可执行文件。
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