RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes [chapter]

Bruno Contreras-Moreira, Jaime A. Castro-Mondragon, Claire Rioualen, Carlos P. Cantalapiedra, Jacques van Helden
2016 Msphere  
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 web site 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, pattern
more » ... ing. 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 annotate the discovered motifs with putative binding factors.
doi:10.1007/978-1-4939-6396-6_18 pmid:27557774 fatcat:fx7wjwfszra2lmsbnucd7ghnmy