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Originally published in Science Express on 29 May 2003
Science 4 July 2003:
Vol. 301. no. 5629, pp. 71 - 76
DOI: 10.1126/science.1084337
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Research Articles

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

Paul Cliften,1 Priya Sudarsanam,1 Ashwin Desikan,1 Lucinda Fulton,2 Bob Fulton,2 John Majors,3 Robert Waterston,1,2 Barak A. Cohen,1 Mark Johnston1*

The sifting and winnowing of DNA sequence that occur during evolution cause nonfunctional sequences to diverge, leaving phylogenetic footprints of functional sequence elements in comparisons of genome sequences. We searched for such footprints among the genome sequences of six Saccharomyces species and identified potentially functional sequences. Comparison of these sequences allowed us to revise the catalog of yeast genes and identify sequence motifs that may be targets of transcriptional regulatory proteins. Some of these conserved sequence motifs reside upstream of genes with similar functional annotations or similar expression patterns or those bound by the same transcription factor and are thus good candidates for functional regulatory sequences.

1 Department of Genetics, 2 Genome Sequencing Center, 3 Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.

* To whom correspondence should be addressed. E-mail: mj{at}genetics.wustl.edu

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