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| Title: | RSAT::Plants: Motif discovery within clusters of upstream sequences in plant genomes |
Authors: | Contreras-Moreira, Bruno CSIC ORCID ; Castro-Mondragón, Jaime A.; Rioualen, Claire; Pérez Cantalapiedra, Carlos CSIC ORCID; van Helden, Jacques | Keywords: | Co-expression DNA motif Position-weight matrix Upstream sequence Cluster |
Issue Date: | Aug-2016 | Publisher: | Springer Nature | Citation: | Contreras-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) | Series: | Methods in Molecular Biology 1482 |
Abstract: | The 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. | Description: | 17 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 | URI: | http://hdl.handle.net/10261/136253 | DOI: | 10.1007/978-1-4939-6396-6_18 | ISBN: | 978-1-4939-6394-2 (Print) 978-1-4939-6396-6 (Online) |
| Appears in Collections: | (EEAD) Libros y partes de libros |
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| Contreras-MoreiraB_MethMolBiol_2016.pdf | 312,45 kB | Adobe PDF |  View/Open |
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