RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes.
Methods Mol Biol
; 1482: 297-322, 2016.
Article
em En
| MEDLINE
| ID: mdl-27557775
ABSTRACT
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 discovery 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.
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1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Biologia Computacional
/
Genômica
/
Imunoprecipitação da Cromatina
Tipo de estudo:
Prognostic_studies
Idioma:
En
Ano de publicação:
2016
Tipo de documento:
Article