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

Olivier Elemento and Saeed Tavazoie*

Author Affiliations

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA

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Genome Biology 2005, 6:R18  doi:10.1186/gb-2005-6-2-r18

Published: 26 January 2005

Abstract

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.