Comparative promoter analysis in vertebrate genomes with the CORG workbench.

ArticleinMethods in Molecular Biology 338:105-18 · February 2006
Impact Factor: 1.29 · DOI: 10.1385/1-59745-097-9:105 · Source: PubMed

    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.