Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach

Genome Biol. 2005;6(2):R18. doi: 10.1186/gb-2005-6-2-r18. Epub 2005 Jan 26.


We describe a powerful new approach for discovering globally conserved regulatory elements between two genomes. The method is fast, simple and comprehensive, without requiring alignments. Its application to pairs of yeasts, worms, flies and mammals yields a large number of known and novel putative regulatory elements. Many of these are validated by independent biological observations, have spatial and/or orientation biases, are co-conserved with other elements and show surprising conservation across large phylogenetic distances.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.
  • Validation Study

MeSH terms

  • Animals
  • Base Sequence
  • Caenorhabditis / genetics
  • Conserved Sequence
  • Drosophila / genetics
  • Genomics / methods*
  • Humans
  • Mice
  • Regulatory Elements, Transcriptional*
  • Saccharomyces / genetics
  • Sequence Alignment
  • Time Factors