Welcome to the SwissRegulon portal ,

a repository of computational biology tools and databases developed by the van Nimwegen lab:

  • SwissRegulon: A database of genome-wide annotations of regulatory sites. We currently have annotations for 17 prokaryotes and 3 eukaroytes in our collection.
  • ISMARA: The Integrated System for Motif Activity Response Analysis is a free online tool that models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For an given input expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets.
  • CRUNCH A completely automated pipe-line for ChIP-seq data analysis, starting from raw sequencing reads, through quality filtering, read mapping, fragment size estimation, peak calling, peak annotation and comprehensive regulatory motif analysis.
  • REALPHY The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data.
  • DWT-toolbox is a collection of software tools for performing motif finding and transcription factor binding site (TFBS) predictions with Dinucleotide Weight Tensors (DWTs).
  • Phylogibbs: An algorithm for inferring regulatory motifs and regulatory sites from collections of DNA sequences, including multiple alignments of orthologous sequences from related organisms. Phylogibbs uses a rigorous Bayesian approach that combines search for overrepresented sequence-motifs with sequence conservation analysis of the putative sites for these motifs.
  • TCS: A data-base of predicted two-component signalling interactions across bacterial genomes.