RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes View Full Text


Ontology type: schema:Chapter      Open Access: True


Chapter Info

DATE

2016-08-25

AUTHORS

Bruno Contreras-Moreira , Jaime A. Castro-Mondragon , Claire Rioualen , Carlos P. Cantalapiedra , Jacques van Helden

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. More... »

PAGES

279-295

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-4939-6396-6_18

DOI

http://dx.doi.org/10.1007/978-1-4939-6396-6_18

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1036724005

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27557774


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