RSAT peak-motifs: Efficient prediction of transcription factor motifs and binding sites from genome-wide sequencing peak sets

Authors

  • Morgane Thomas-Chollier Institut de Biologie de l'Ecole Normale Supérieure, Paris
  • Matthieu Defrance Centro de Ciencias Genomicas, Universidad Nacional Autónoma de México, Cuernavaca
  • Olivier Sand CNRS-UMR8199 Institut de Biologie de Lille, Lille
  • Carl Herrman INSERM U928 & Université de la Méditerranée, Marseille
  • Denis Thieffry Institut de Biologie de l'Ecole Normale Supérieure, Paris
  • van Helden Jacques INSERM U928 & Université de la Méditerranée, Marseille

DOI:

https://doi.org/10.14806/ej.19.A.629

Keywords:

cis-regulatory element, ChIP-seq, motif discovery

Abstract

Peak-motifs is a computational pipeline that discovers motifs in peak sequences, compares them with databases, exports putative binding sites for visualization in the UCSC genome browser and generates an extensive report suited for both naive and expert users. It relies on time- and memory-efficient algorithms enabling the treatment of several thousand peaks within minutes. Peak-motifs not only finds motifs associated the ChiPed factor, but usually further returns motifs potentially bound by cofactors.

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Published

2013-04-08

Issue

Vol. 19: Supplement A

Section

Oral Presentations

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