Finding functional features in Saccharomyces Genomes by phylogenetic footprinting
Supplement to the ArticlePaul Cliften 1, Priya Sudarsanam 1, Ashwin Desikan 1, Lucinda Fulton 2, Bob Fulton 2, John Majors 3, Robert Waterston 4, Barak A. Cohen 1, Mark Johnston 1
Abstract
The sifting and winnowing of DNA sequence that occurs during evolution causes non-functional 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.
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Supplements to Figures | |
| - Supporting Online Material (from Science) | ||
| - Supplement to Figure 1 (nucleotide conservation for long promoters and divergently transcribed promoters) | ||
| - Significance Tests for promoter conservation versus distance | ||
| -Occurences of Known and Unknown Motifs. | ||
| - Expression Coherence results for known promoter motifs | ||
| - Lists of False and Questionable ORFs | ||
| - Small conserved ORFs | - FASTA file of small ORF DNA | |
| - FASTA file of small ORF translations | ||
| - Example of a conserved 5' UTR sequence | ||
| - Example of a promoter alignment showing conserved sequence motifs | ||
