Nature Biotechnology 23, 1249 - 1256 (2005)
Published online: 6 October 2005; | doi:10.1038/nbt1140
Discovery of regulatory elements in vertebrates through comparative genomicsAmol Prakash1
& Martin Tompa1, 21
Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195-2350, USA. 2
Department of Genome Sciences, Box 357730, University of Washington, Seattle, Washington 98195-7730, USA.
Correspondence should be addressed to Martin Tompa tompa@cs.washington.edu We have analyzed issues of reliability in studies in which comparative genomic approaches have been applied to the discovery of regulatory elements at a genome-wide level in vertebrates. We point out some potential problems with such studies, including difficulties in accurately identifying orthologous promoter regions. Many of these subtle analytical problems have become apparent only when studying the more complex vertebrate genomes. By determining motif reliability, we compared existing tools when applied to the discovery of vertebrate regulatory elements. We then used a statistical clustering method to produce a computational catalog of high quality putative regulatory elements from vertebrates, some of which are widely conserved among vertebrates and many of which are novel regulatory elements. The results provide a glimpse into the wealth of information that comparative genomics can yield and suggest the need for further improvement of genome-wide comparative computational techniques.
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