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Twine: display and analysis of cis-regulatory modules.
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PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.
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SPACER: identification of cis-regulatory elements with non-contiguous critical residues.
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An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale.
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TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments.
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ClutrFree: cluster tree visualization and interpretation.
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Nsite, NsiteH and NsiteM computer tools for studying transcription regulatory elements.
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SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides.
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引用本文的文献

3
Enhancer diversity and the control of a simple pattern of Drosophila CNS midline cell expression.
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Screening for protein-DNA interactions by automatable DNA-protein interaction ELISA.
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1
RSAT 2011: regulatory sequence analysis tools.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W86-91. doi: 10.1093/nar/gkr377.
2
Enhancer function: new insights into the regulation of tissue-specific gene expression.
Nat Rev Genet. 2011 Apr;12(4):283-93. doi: 10.1038/nrg2957. Epub 2011 Mar 1.
3
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system.
Nucleic Acids Res. 2011 Jan;39(Database issue):D111-7. doi: 10.1093/nar/gkq858. Epub 2010 Nov 19.
4
MochiView: versatile software for genome browsing and DNA motif analysis.
BMC Biol. 2010 Apr 21;8:49. doi: 10.1186/1741-7007-8-49.
5
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.
Nucleic Acids Res. 2010 Jan;38(Database issue):D105-10. doi: 10.1093/nar/gkp950. Epub 2009 Nov 11.
6
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.
Bioinformatics. 2009 Oct 15;25(20):2730-1. doi: 10.1093/bioinformatics/btp472. Epub 2009 Aug 4.
7
A survey of DNA motif finding algorithms.
BMC Bioinformatics. 2007 Nov 1;8 Suppl 7(Suppl 7):S21. doi: 10.1186/1471-2105-8-S7-S21.
8
ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors.
Bioinformatics. 2007 Apr 15;23(8):1032-4. doi: 10.1093/bioinformatics/btm047. Epub 2007 Feb 18.
9
GenePalette: a universal software tool for genome sequence visualization and analysis.
Dev Biol. 2004 Jul 15;271(2):431-8. doi: 10.1016/j.ydbio.2004.04.011.
10
A regulatory code for neurogenic gene expression in the Drosophila embryo.
Development. 2004 May;131(10):2387-94. doi: 10.1242/dev.01124.

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