RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes [chapter]

Jaime A. Castro-Mondragon, Claire Rioualen, Bruno Contreras-Moreira, Jacques van Helden
2016 Msphere  
In this protocol we explain how to run ab initio motif discovery in order to gather putative transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP-seq experiments. The protocol starts from a set of peak coordinates (genomic regions) which can be either downloaded from ChIP-seq databases, or produced by a peak-calling software tool. We provide a concise description of the successive steps to discover motifs, cluster the motifs returned by different motif
more » ... ery algorithms, and compare them with reference motif databases. The protocol is documented with detailed notes explaining the rationale underlying the choice of options. The interpretation of the results is illustrated with an example from the model plant Arabidopsis thaliana.
doi:10.1007/978-1-4939-6396-6_19 pmid:27557775 fatcat:uf4jvjkdw5ed5h4jy6bhwui3si