#cparse("/super/config/super.config.vm") #cparse("${superIncludes}/super.before-doctype.fhtml") #cparse("${superIncludes}/super.head-top.fhtml") Supplementary Information - Kellis et al - Duplication #cparse("${superIncludes}/super.head-bottom.fhtml") #cparse("${superIncludes}/super.body-top.fhtml")
Directory Filename Type Size Comment
All_Data Kellis_Duplication zip 30 Mb Download all supplementary information (30Mb compressed, 70 Mb uncompressed)
S1_Assembly Assembly_stats xls 16 kb Description of assembly, scaffolds, contigs, and chromosomes

Kwal_contigs fasta 10,797 kb The raw nucleotide sequence of all contigs

Kwal_scaffolds txt 14 kb Scaffolds (supercontigs) giving relative order, orientation, and spacing of contigs
S2_ORFs predicted_ORFs fasta 7,459 kb Raw nucleotide sequence of all predicted Open Reading Frames (ORFs)

predicted_proteins fasta 2,528 kb Protein translation of all Open Reading Frames (ORFs)
S3_Annotation Kwal_forward txt 993 kb Annotation of each K. waltii gene and its best match to S. cerevisiae (forward:  Kwal => Scer)

Kwal_forward_full txt 1,482 kb Annotation of each K. waltii gene and all its matches to S. cerevisiae (forward:  Kwal => Scer)

Kwal_homology_groups_large txt 105 kb Gene families (groups of genes with ambiguous correspondence) that contain at least 4 members

Kwal_homology_groups_small txt 182 kb Gene families (groups of genes with ambiguous correspondence) that contain 3 members of fewer

Kwal_reverse txt 776 kb Coordinates of each S. cerevisiae gene and its best match in K. waltii (reverse:  Kwal <= Scer)

Kwal_reverse_full txt 1,086 kb Coordinates of each S. cerevisiae gene and all its matches in K. waltii (reverse:  Kwal <= Scer)
S4_Blocks Kwal_synteny_blocks txt 28 kb Blocks of conserved gene order (synteny) between the two species

Matches_by_chromosome xls 420 kb Gene correspondence, grouped by chromosome (shows duplicate mapping)

Matches_by_chromosome_with_syn xls 480 kb Gene correspondence, grouped by chromosome with synteny block information

Paired_regions xls 100 kb Paired regions in S. cerevisiae as defined by blocks of doubly conserved synteny (DCS)
S5_Poster all_scaffolds pdf 1,200 kb Detailed visualization of gene correspondence for every K. waltii chromosome

poster pdf 1,127 kb Detailed visualization of gene correspondence for all K. waltii chromosomes (single page)
S6_Visualization all_tiles html 257 kb Detailed visualization of paired sister regions interleaved with K. waltii in 253 DCS blocks

tile_000 jpg 71 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_001 jpg 74 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_002 jpg 120 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_003 jpg 119 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_004 jpg 122 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_005 jpg 113 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_006 jpg 120 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_007 jpg 119 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_008 jpg 104 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_009 jpg 107 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_010 jpg 129 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_011 jpg 78 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_012 jpg 52 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_013 jpg 125 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_014 jpg 105 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_015 jpg 115 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_016 jpg 122 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_017 jpg 73 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_018 jpg 77 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_019 jpg 129 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_020 jpg 38 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_021 jpg 71 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_022 jpg 128 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_023 jpg 107 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_024 jpg 97 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_025 jpg 57 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

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tile_250 jpg 79 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_251 jpg 115 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions

tile_252 jpg 80 kb Tiling of K. waltii genome in duplicate regions.  See all_tiles.html for index of genes in duplicate regions
S7_DupBlocks scer_pairs_01 pdf 9 kb S. cerevisiae chromosome 1, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_02 pdf 12 kb S. cerevisiae chromosome 2, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_03 pdf 11 kb S. cerevisiae chromosome 3, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_04 pdf 14 kb S. cerevisiae chromosome 4, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_05 pdf 12 kb S. cerevisiae chromosome 5, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_06 pdf 11 kb S. cerevisiae chromosome 6, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_07 pdf 14 kb S. cerevisiae chromosome 7, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_08 pdf 12 kb S. cerevisiae chromosome 8, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_09 pdf 12 kb S. cerevisiae chromosome 9, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_10 pdf 13 kb S. cerevisiae chromosome 10, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_11 pdf 12 kb S. cerevisiae chromosome 11, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_12 pdf 14 kb S. cerevisiae chromosome 12, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_13 pdf 13 kb S. cerevisiae chromosome 13, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_14 pdf 12 kb S. cerevisiae chromosome 14, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_15 pdf 13 kb S. cerevisiae chromosome 15, connected with its sister regions in S. cerevisiae chromosomes

scer_pairs_16 pdf 13 kb S. cerevisiae chromosome 16, connected with its sister regions in S. cerevisiae chromosomes
S8_DupGenes Browse html 141 kb Browse three-way nucleotide/protein/translation alignments for all 457 gene pairs

protein tgz 545 kb Download all protein alignments

nucleotide tgz 977 kb Download all nucleotide alignments

translate tgz 961 kb Download all frame-aware nucleotide alignments (nucleotide alignments that preserve translation)

YAL015C_YOL043Cp txt 2 kb Alignment for duplicated gene pair and its K. waltii ortholog (p = protein)

YAL015C_YOL043Ct txt 6 kb Alignment for duplicated gene pair and its K. waltii ortholog (t = translate.  Nucleotide alignment that preserves translation)

YAL017W_YOL045W txt 21 kb Second gene pair => Nucleotide

YAL017W_YOL045Wp txt 7 kb Second gene pair => Protein

YAL017W_YOL045Wt txt 21 kb Second gene pair => Frame-aware nucleotide

YAL023C_YOR321W txt 11 kb (... and so on ...)

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Browse all alignments (nucleotide / protein/ translate)

YOR256C_YPL176C txt 12 kb 457th gene pair => Nucleotide

YOR256C_YPL176Cp txt 4 kb 457th gene pair => Protein

YOR256C_YPL176Ct txt 12 kb 457th gene pair => Frame-aware nucleotide
S9_Trees Tree_lengths_protein txt 25 kb Protein-divergence branch lengths for gene pairs with S. bayanus and K. waltii orthologs

Fiveway_trees txt 169 kb Protein-divergence trees for gene pairs with S. bayanus and K. waltii orthologs

Duplicated_Pairs xls 269 kb Protein divergence absolute and relative rates for all pairs and their K. waltii ortholog

Nucleotide_Divergence xls 202 kb Nucleotide divergence absolute and relative rates for all pairs and their K. waltii ortholog
S10_Centromeres Centromeres xls 17 kb K. waltii centromere location, sequence and pairing with S. cerevisiae

Chr6_16 jpg 69 kb Visualization of K. waltii centromere 1 and its pairing with Cen6:Cen16 in S. cerevisiae

Chr2_4 jpg 117 kb Visualization of K. waltii centromere 2 and its pairing with Cen2:Cen4 in S. cerevisiae

Chr2_4b jpg 62 kb Visualization of K. waltii centromere 2 and its pairing with Cen2:Cen4 in S. cerevisiae

Chr8_11 jpg 112 kb Visualization of K. waltii centromere 3 and its pairing with Cen8:Cen11 in S. cerevisiae

Chr1_7 jpg 97 kb Visualization of K. waltii centromere 4 and its pairing with Cen1:Cen7 in S. cerevisiae

chr_10_12 jpg 100 kb Visualization of K. waltii centromere 5 and its pairing with Cen10:Cen12 in S. cerevisiae

Chr5_9 jpg 123 kb Visualization of K. waltii centromere 6 and its pairing with Cen5:Cen9 in S. cerevisiae

chr13_15 jpg 127 kb Visualization of K. waltii centromere 7 and its pairing with Cen13:Cen15 in S. cerevisiae

chr3_14 jpg 111 kb Visualization of K. waltii centromere 8 and its pairing with Cen3:Cen14 in S. cerevisiae

Telomere_hits_all xls 947 kb Blast hits of telomeric repeat elements against K. waltii and S. cerevisiae



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