The Analysis of Regulatory Sequences

Warning

This web site contains support material for the course on the Analysis of Regulatory Sequences.

Site

http://rsa-tools.github.io/course/ source repository

Author

Jacques van Helden
ORCID 0000-0002-8799-8584
jacques.van-helden@univ-amu.fr

Book chapter

Pre-print version of a book chapter for a course given in Les Houches (2004).

Slides

Transcriptional regulation
Sequence models
Position-specific scoring matrices
Transcription factor databases
Pattern matching
   Introduction
   String-based pattern matching
   Matrix-based pattern matching
   Probability distributions of matrix scores (matrix-distrib)
   Empirical distributions of matrix scores (matrix-quality).
   Detection of cis-regulatory modules (CRMs)
Motif discovery
   Introduction: motif discovery
   String-based motif discovery
   K-mer count statistics
   Matrix-based motif discovery
   Genome-scale motif discovery
Evaluation of discoverd motifs
   Motif comparisons
   Evaluating pattern matching and motif discovery results
Classifying gene promoters (upstream non-coding sequences) based on motif counts
Analysis of tanscriptomic data
   Introduction to DNA chips
   Analysis of regulatory regions from clusters of co-expressed genes
Comparative genomics
Phylogenetic footprints (intro)
Discovering phylogenetic footprints in bacterial genomes
Inferring groups of functionally related genes
Hgh-throughput sequencing
peak-motifs: detecting motifs in large sets of ChIP-seq peak sequences
Acknowledgements
Short presentation