Supplementary information

    Sequencing and Comparison of Yeasts to Identify Genes and Regulatory Elements
    Manolis Kellis, Nick Patterson, Matthew Endrizzi, Bruce Birren, Eric Lander

S1. Sequences and Alignments

S2. Annotation

S3. Visualization of gene correspondence

    S3a Dotplots S.paradoxus S.mikatae S.bayanus Dotplots of gene correspondence
    S3b Tiling Example Figure 1 showing S. cerevisiae Chromosome VII
    Visualization 250 files tiling the S.cerevisiae genome (jpg/ps/matlab)
    S3c Interactive Synteny viewer Interactive synteny viewer can be found at the SGD site

S4. Mutation Counts

    S4aMutationCounts(xls)68 kb Overall counts of transitions, transversions, insertions, deletions along phylogenetic tree
    S4bKaKs_average(xls)435 kb Ka/Ks rate for uninterrupted S. cerevisiae ORFs
    S4bKaKs_details(xls)834 kb Ka/Ks rate for uninterrupted S. cerevisiae ORFs (all pairwise comparisons)

S5. Rearrangements

S6. RFC test

S7. Revisiting S. cerevisiae annotation

S8. Genome-wide motifs

    S8aTopMinis(txt)164 kb Table of mini-motifs with CC1, CC2, CC3 score, extension and conservation counts
    AllMinis(txt)335 kb
    S8bCC1_collapsing(txt)179 kb Sequence-based motif collapsing for each test
    CC2_collapsing(txt)137 kb
    CC3_collapsing(txt)167 kb
    S8cMegaRecollapsing(xls)313 kb Co-occurence-based collapsing of grouped consensi
    S8dGenesHit(txt)1.5 Mb Genes containing each genome-wide motif (upstream)
    GenesHit_down(txt)1.5 Mb Genes containing each genome-wide motif (downstream)

S9. Category-based motif discovery

    S9aIncreased_Enrichment(xls)25 kb Increased enrichment of known motifs by using multiple genomes
    S9bComparison_with_MEME(xls)24 kb Comparison of our category-based motif discovery and MEME for known motifs
    S9cCategory_Based_Novel(xls)48 kb All category-based motifs discovered, clustered by sequence similarity