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Title

RSAT::Plants: Motif discovery within clusters of upstream sequences in plant genomes

AuthorsContreras-Moreira, Bruno ; Castro-Mondragón, Jaime A.; Rioualen, Claire; Pérez Cantalapiedra, Carlos ; van Helden, Jacques
KeywordsCo-expression
DNA motif
Position-weight matrix
Upstream sequence
Cluster
Issue DateAug-2016
PublisherSpringer
CitationContreras-Moreira B, Castro-Mondragon JA, Rioualen C, Cantalapiedra CP, van Helden J. RSAT::Plants: Motif discovery within clusters of upstream sequences in plant genomes. In: Hehl R (ed.), Plant Synthetic Promoters (Methods in Molecular Biology 1482: 279-295), New York, Springer Science+Business Media. DOI: 10.1007/978-1-4939-6396-6_18 (2016)
SeriesMethods in Molecular Biology
1482
AbstractThe plant-dedicated mirror of the Regulatory Sequence Analysis Tools (RSAT, http://​plants.​rsat.​eu) offers specialized options for researchers dealing with plant transcriptional regulation. The website contains whole-sequenced genomes from species regularly updated from Ensembl Plants and other sources (currently 40), and supports an array of tasks frequently required for the analysis of regulatory sequences, such as retrieving upstream sequences, motif discovery, motif comparison, and pattern matching. RSAT::Plants also integrates the footprintDB collection of DNA motifs. This protocol explains step-by-step how to discover DNA motifs in regulatory regions of clusters of co-expressed genes in plants. It also explains how to empirically control the significance of the result, and how to associate the discovered motifs with putative binding factors.
Description17 Pags.- 4 Tabls.- 2 Figs. The definitive version is available at: http://link.springer.com/bookseries/7651 and http://link.springer.com/book/10.1007/978-1-4939-6396-6
Publisher version (URL)http://dx.doi.org/10.1007/978-1-4939-6396-6_18
URIhttp://hdl.handle.net/10261/136253
DOI10.1007/978-1-4939-6396-6_18
ISBN978-1-4939-6394-2 (Print)
978-1-4939-6396-6 (Online)
Appears in Collections:(EEAD) Libros y partes de libros
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