Web site for this course



Abbrev Name
JCM Jaime Castro Mondragon
DP Denis Puthier
JvH Jacques van Helden


Resource Link
Glossary concept definitions
Regulatory Sequence Analysis Tools (RSAT) http://rsat.eu/
RSAT teaching material http://rsa-tools.github.io/teaching/
RSAT course (slides) http://rsa-tools.github.io/course/
footprintDB http://floresta.eead.csic.es/footprintdb/
MEME suite http://meme-suite.org/

Content table

Date From To Subject Teacher Practicals
Mon 17/10 09:00 10:30 Characterizing and representing TF-DNA interactions
(from sites to motifs)
JvH [01.2_regulatory_sequences_intro]
[tutorial from sites to motifs]
Mon 17/10 11:00 12:30 Introduction to motif database JvH [footprintDB]
Mon 17/10 14:00 15:30 ChIP-seq analysis DP [slides]
[tutorial mapping]
Wed 21/10 16:00 17:30 ChIP-seq analysis DP [tutorial peak annotation]
[tutorial peak-motifs]
Tue 18/10 09:00 10:30 Scanning sequences to predict binding sites
(from motifs to sites)
JvH [01.4.PSSM_theory]
[RSAT] dna-pattern, matrix-scan, permute-matrix, random-seq
[tutorial E.coli promoter scanning]
Tue 18/10 15:10 16:55 ENCODE JvH [tutorial: ENCODE ChIP-seq peaks]
Wed 19/10 14:00 15:30 Discovering motifs in regulatory sequences
(from sequences to motifs)
JvH [03.2.1.pattern_discovery_strings]
[RSAT] oligo-analysis, dyad-analysis, position-analysis, random-genes
Wed 19/10 16:00 17:30 Motif comparison and clustering JvH + JCM [RSAT] matrix-clustering
[tutorial matrix-clustering]

White/green board pictures