A suite of web-based programs to search for transcriptional regulatory motifs
Stanford Medical Informatics, 251 Campus Drive X215, 1 Department of Computer Science and 2 Department of Biochemistry, Stanford University, Stanford, CA 94305, USA, 3 Center of Bioinformatics, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China, 4 Department of Statistics, Harvard University, Cambridge, MA 02138, USA, and 5 Department of Biostatistics, Harvard School of Public Health, Dana-Farber Cancer Institute, Boston, MA 02115, USA
* To whom correspondence should be addressed. Tel: +1 617 632 2472; Fax: +1 617 632 2444; Email: xsliu{at}jimmy.harvard.edu
Received February 15, 2004; Revised and Accepted April 27, 2004
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.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. A. F. T. van Hijum, M. H. Medema, and O. P. Kuipers Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation Microbiol. Mol. Biol. Rev., September 1, 2009; 73(3): 481 - 509. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Ji, W. Li, J. Song, L. Wei, and X. S. Liu CEAS: cis-regulatory element annotation system. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W551 - W554. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Ranjan, J. Seshadri, V. Vindal, S. Yellaboina, and A. Ranjan iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W584 - W587. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Suzuki, M. G. Ketterling, and D. R. McCarty Quantitative Statistical Analysis of cis-Regulatory Sequences in ABA/VP1- and CBF/DREB1-Regulated Genes of Arabidopsis Plant Physiology, September 1, 2005; 139(1): 437 - 447. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Xie, E. Allen, N. Fahlgren, A. Calamar, S. A. Givan, and J. C. Carrington Expression of Arabidopsis MIRNA Genes Plant Physiology, August 1, 2005; 138(4): 2145 - 2154. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Albano, W. K. Smits, L. T. Y. Ho, B. Kraigher, I. Mandic-Mulec, O. P. Kuipers, and D. Dubnau The Rok Protein of Bacillus subtilis Represses Genes for Cell Surface and Extracellular Functions J. Bacteriol., March 15, 2005; 187(6): 2010 - 2019. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Tang, S. L. Tan, S. K. Ramadoss, A. P. Kumar, M.-H. E. Tang, and V. B. Bajic Computational method for discovery of estrogen responsive genes Nucleic Acids Res., December 1, 2004; 32(21): 6212 - 6217. [Abstract] [Full Text] [PDF]
|
|