Finding functional features in Saccharomyces genomes by phylogenetic footprinting

Paul Cliften, Priya Sudarsanam, Ashwin Desikan, Lucinda Fulton, Bob Fulton, John Majors, Robert Waterston, Barak A. Cohen, Mark Johnston

Research output: Contribution to journalArticle

685 Scopus citations


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.

Original languageEnglish
Pages (from-to)71-76
Number of pages6
Issue number5629
StatePublished - Jul 4 2003

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