Web-services

  • 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 procedure for ChIP-seq data analysis, starting from raw read quality control, through read mapping, peak detection and annotation, and including comprehensive DNA sequence motif analysis
  • SwissRegulon A database of genome-wide annotations of regulatory sites. We currently have annotations for 17 prokaryotes and 3 eukaroytes in our collection.
  • 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.
  • RealPhy The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data.
  • TCS A data-base of predicted two-component signalling interactions across bacterial genomes.