MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
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* Corresponding author: Michael B Eisen mbeisen@lbl.gov
Genome Biology 2004, 5:R98 doi:10.1186/gb-2004-5-12-r98
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Tools for simulating evolution of aligned genomic regions with integrated parameter estimation Avinash Varadarajan, Robert K Bradley, Ian H Holmes Genome Biology 2008, 9:R147 (8 October 2008) Three tools for simulating genome evolution are presented: for neutrally evolving DNA, for phylogenetic context-free grammars and for richly structured syntenic blocks of genome sequence. |
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Christof Francke, Robert Kerkhoven, Michiel Wels, Roland J Siezen BMC Genomics 2008, 9:145 (27 March 2008) |
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From biophysics to evolutionary genetics: statistical aspects of gene regulation Michael Lässig BMC Bioinformatics 2007, 8(Suppl 6):S7 (27 September 2007) |
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Finding regulatory elements and regulatory motifs: a general probabilistic framework Erik van Nimwegen BMC Bioinformatics 2007, 8(Suppl 6):S4 (27 September 2007) |
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WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences Giulio Pavesi, Federico Zambelli, Graziano Pesole BMC Bioinformatics 2007, 8:46 (7 February 2007) |
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PhyloScan: identification of transcription factor binding sites using cross-species evidence C Steven Carmack, Lee McCue, Lee A Newberg, Charles E Lawrence Algorithms for Molecular Biology 2007, 2:1 (23 January 2007) |
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XRate: a fast prototyping, training and annotation tool for phylo-grammars Peter S Klosterman, Andrew V Uzilov, Yuri R Bendaña, Robert K Bradley, Sharon Chao, Carolin Kosiol, Nick Goldman, Ian Holmes BMC Bioinformatics 2006, 7:428 (3 October 2006) |
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Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen BMC Bioinformatics 2006, 7:376 (14 August 2006) |