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.
    • CREMA The Cis-Regulatory Element Motif Activity analysis infers key transcriptional regulators driving chromatin changes across any number of samples. For every reguator it predicts which genes are most likely targeted and infers functional pathways.
  • REALPHY The Reference sequence Alignment based Phylogeny builder is a free online pipeline that infers 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.