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Discovery of Conserved Motifs in Promoters of Orthologous Genes in Prokaryotes

  • Rekin’s Janky
  • Jacques van Helden
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)

Summary

We present a method to predict cis-acting elements for a given gene by detecting over-represented motifs in promoters of a set of ortholo gous genes in prokaryotes (single-gene, multiple-genomes approach). The method has been used successfully to detect regulatory elements at various taxonomical levels in prokaryotes. A web interface is available at the Regulatory Sequence Analysis Tools site (http://rsat.scmbb.ulb.ac.be/rsat/).

Key Words

Transcriptional regulation pattern discovery pattern matching phylogenetic footprinting prokaryotes RSAT get-orthologs retrieve-seq dyad-analysis 

Notes

Acknowledgments

This work was supported by a doctoral grant from Fonds pour la Recherche dans l'Industrie et l'Agriculture (F.R.I.A.) to RJ and by the “BioSapiens Network of Excellence” funded under the sixth Framework programme of the European Communities (LSHG-CT-2003-503265). Genome installation and orthologs identification are done on a 40-node PC cluster contributed by various institutions, including the Belgian Fonds pour la Recherche Fondamentale Collective (F.R.F.C. grant 2005). We are grateful to Raphaël Leplae for his enthusiasm in obtaining, installing, and maintaining this cluster. JvH acknowledges Stéphane Vissers for an inspiring discussion on the importance of good quality protocols for teaching and practicing good science. We are thankful to Stephan Kurtz for making available his very efficient program vmatch, which we use to purge redundant fragments.

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Rekin’s Janky
    • 1
  • Jacques van Helden
    • 2
  1. 1.Universite Libre de BruxellesBrusselsBelgium
  2. 2.Service de Conformation des Macromolécules Biologiques et de Bioinformatique (SCMBB)Université Libre de BruxellesBrusselsBelgium

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