The Analysis of Regulatory Sequences


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



Jacques van Helden

Book chapter

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


Transcriptional regulation
Sequence models
Position-specific scoring matrices
Transcription factor databases
Pattern matching
   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)
Pattern discovery
   String-based pattern discovery
   Word count statistics
   Matrix-based pattern discovery
   Genome-scale pattern discovery
Evaluation of pattern predictions
   Motif comparisons
   Evaluating pattern matching and pattern discovery results
Gene classification on the basis of upstream motifs
Analysis of gene expression data
   Introduction to DNA chips
   Analysis of regulatory regions from DNA chip clusters
Comparative genomics
Phylogenetic footprints (intro)
Discovering phylogenetic footprints in bacterial genomes
Inference of clusters of functionally related genes
Hgh-throughput sequencing
peak-motifs: detecting motifs in large sets of ChIP-seq peak sequences
Short presentation