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Comparative Promoter Analysis in Vertebrate Genomes With the CORG Workbench

  • Christoph Dieterich
  • Martin Vingron
Part of the Methods in Molecular Biology book series (MIMB, volume 338)

Abstract

CORG is a versatile web-based workbench for comparative promoter analysis in vertebrate model organisms. Two kinds of information are explicitly considered in the automated annotation process. First, local conservation patterns in upstream regions of homologous genes: These phylogenetic footprints are likely to stem from sequence elements that are under selective pressure. The CORG pipeline detects and exploits patterns of local similarity to annotate promoter regions. Second, experimental data on transcription start sites: exon positions and DNA binding site descriptions complete the promoter annotation. These data are made available via an interactive web portal. Individual promoter studies are supported by a JAVA applet that supplies all data down to the nucleotide level.

Key Words

Promoter phylogenetic footprinting vertebrates comparative sequence analysis regulatory elements DNA binding site conserved promoter elements sequence alignment 

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Copyright information

© Humana Press Inc. 2006

Authors and Affiliations

  • Christoph Dieterich
    • 1
  • Martin Vingron
    • 2
  1. 1.Computational Molecular Biology DepartmentMax Planck Institute for Molecular GeneticsBerlinGermany
  2. 2.Max Planck Institute for Molecular GeneticsGermany

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