Multiz Alignments of 7 Yeasts
 

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Place cursor over species for alignment detail. Click on 'B' to link to browser for aligned species, click on 'D' to get DNA for aligned species.
Alignment block 1 of 9 in window, 194903 - 195104, 202 bps 
B D  S. cerevisiae  ctttctactggaacttcgttcaatggagcatgttcatactttctttctttcctggtagtctcttttgcaa
            sacPar  cctcctagtggagcttcactcaatggagcatgttcgtgctttacttcttttctgatggcttcttctgtag
            sacMik  tcttctgctgcagcttccttgagtggagtatgatcgagtttccttccgtttctgacagcttcttcttttg
            sacKud  tctctcgttagagcttcccctagaggtgcatcctcatgctttccttcttttgtgataaattcttctttag
            sacBay  -----cgctggagcatcatcgagtgcaatatcgtcatgttttccttcttttgtgataacttgttctgctg

     S. cerevisiae  aagcagaaccatcttgcgaaatagctgttttaggggaaggaaacgttacattaccttttaaagaaggagt
            sacPar  aagcaggaccattttgtaaattcgctgctttggaagaagcgaatttcatgctgctttttagagaaggagt
            sacMik  gtgcctgttcgatttgtgaacttcctgctttagaagaagcaattgtcgtgttgccttttaaggacggagt
            sacKud  gagcagctttgccttggaaatcttctgaattagaggaagcaggtgacttatcgcctttaagggagggcgt
            sacBay  gaacaggttcgcttcgggaactttctggattagaagaagctgccgtcttgacatcttttaaagagggagt

     S. cerevisiae  tggcgtctcagggccctcatagtacaactctgacccattttcatttgtattgtgtgcagttt
            sacPar  tggcgtcgcaggaccctcataatacagctctgactcatctttatttgcttcgtgtgcagctt
            sacMik  tggagtctcaggaccttcataatacaaccctaatccatcattgtttgcttcttgcgcagatt
            sacKud  tggcgtatcaggaccttcaccatacaactctgacccactttttgtcgcttcacttgtagatt
            sacBay  tggcgtctcagggccttcatcgtacaaaccctgctcattgttttcttcttcttttgtatctt

Alignment block 2 of 9 in window, 195105 - 195112, 8 bps 
B D  S. cerevisiae  tgtcgccc
            sacPar  tgtcactc
            sacKud  tgtcatcc
            sacBay  tgtcatcc

Alignment block 3 of 9 in window, 195113 - 195163, 51 bps 
B D  S. cerevisiae  tcgtccttttcttcaccagcgcttccgccgtcctcttc-----------------gttatttaaagta-
            sacPar  tctctcctttcctcatttgcgcttccgccatcttcatt-----------------attgcttaaggtg-
            sacKud  tccccctttcccccattaacaaatgtcccgtcttcact-----------------gttatccaaagtg-
            sacBay  tccttgttttccttttcttcatttgtgtcatcctcctt-----------------gctctccagcgta-
            sacKlu  ttgcccttcgcttcagttgttttttcgctttcctcgtttgaaggaagtaattcacgcttgtttaaatat

Alignment block 4 of 9 in window, 195164 - 195447, 284 bps 
B D  S. cerevisiae  gcaacattgttttcattgctgtgctcgtccacctcctttggatactcatcatcggcaaaccagttaccgt
            sacPar  gcaacattattttcgttgctatgctcgtcaatttcttttggatactcatcatcggcaaaccagttaccat
            sacMik  gcaacattattctcattgctatgctcgtcaatctccttcgcatactcatcatcggcaaaccagttaccat
            sacKud  gcaacattattttcgttactatgttcatcaacctcttttggatactcatcatcggcaaaccagttgccat
            sacBay  gtcacattattttcgttactatgttcgtcaatctcctttggatactcgtcatcggcaaaccagttgccat
            sacKlu  aaaacattgttttcattcccacgatcgtcaatctccttagcaaaattgtcatcggtaaaccagtttccat

     S. cerevisiae  tctgatctataaatttgaaatgtaccttatctttatcattatgtttggttaccgaagatt----------
            sacPar  tctgatctataaatttaaaatggaccttatctttatcgttatgtttagttgtcgaagatt----------
            sacMik  tgtgatctataaacttgaaatgtaccttatccttatcattatgtttggctatagaagatt----------
            sacKud  tctgatctatgaatttaaaatgcaccttgtccttatcatcatatttggttatcgaagaat----------
            sacBay  tgtgatctataaatttaaaatgtaccttg------tcgtcgtgtttagttgtcgatgatt----------
            sacKlu  ctccatcaataaatttgaaatggattttgaat---tcgttatccccaatagcaaaggatttcaatttttc

     S. cerevisiae  --catcaaatttgtattcccatttcccgctactggtatttattttcatgggtacaccttcccaattggta
            sacPar  --catcaaattcgtattcccatttcccactatcagtatttattttcatgggtacaccttcccaatcggta
            sacMik  --catcgattttatattcccattgtccagtttcggcattaatactcatgggcacacctttccaatcggta
            sacKud  --catggaacctatactcccactttccagtatcaacattaatttccatgggcacaccttcccagttggtg
            sacBay  --catcaaatgtatactcccactttccggaatcatcattaatttccatgggcataccttcccaattggtg
            sacKlu  tgtatcgagattgtactcccattgctttgaatcgtcctgataatgcattggtacaatagcccaatcggtg

     S. cerevisiae  aactccccagcgatcttcaactctggaaagtcttccg----ccggatgatcaaatacaa----------t
            sacPar  aactccccagcgattttcaaatctggaaagtcctccg----cagaatgatcaaaaacaa----------t
            sacMik  aattcgccagcgatcttcaaacctggaaagtcttccg----caggatgaggaaatacaa----------t
            sacKud  aactcgccagcaattttcaaatctggaaagtcatccg----caggatgatcaaatacaa----------t
            sacBay  aattcgccagcaatcttcaagtctgggaagtcatccg----ctgggtgatcaaaaacga----------t
            sacKlu  aaatcaccggcgactttcaa----ggcacttgctccgtttccggagtgcttaaaaatgatcttactcatt

     S. cerevisiae  ggtgaccattatttagttgctttgcctatc
            sacPar  ggtgaccattacttactagctttgcctatc
            sacMik  ggtgaccattacttactaactctggctatc
            sacKud  agtgaccattactaactaacttttgctatc
            sacBay  ggtgaccattattta-taactttacctatc
            sacKlu  gctggtctttactcggaaaaattactgatc

Alignment block 5 of 9 in window, 195448 - 195701, 254 bps 
B D  S. cerevisiae  t--taatgttacaaccaagta-tgtatgtatgtacgtacgtat--gcaaagaagtggatatagagaagga
            sacPar  t--tattgttacaaccaagta-tatatgtatgtatgtatgtat--gcaaagaagtggatatagaagagga
            sacMik  t--tgttgttacaatcaa-----ctatgtatatatgtatgtat--gcaaagaaat------------aga
            sacKud  t--tatgattaca--ctgttactacagcaaaatatgtatatat--gctaagaactagataaaaattagga
            sacBay  ttctattattata--cttttactacaaccaaagatttatgtgtaggtaaagaa-tagacagaaagatgaa

     S. cerevisiae  aagtaggggagagagggaaagaacaaaaaaattgaagttatt-tgagatagtcttgtattatttatctgt
            sacPar  aagtaggggagagaaggaaagaacaagaatatagaagttattataagtaaatagtgtattatttatctat
            sacMik  aagtaggggagaaaaggaaag--taaaaatctacaagttgtattaagtggttcttgtattatttatcttt
            sacKud  aagcagggaagagaaggaaaa--caaaaatatataagttattttgagc-ggtcttgaattatttatctgt
            sacBay  aagcaag--aaggaaggaaag--caa-aatatacaagtgattttgggt-aatcctttactatttatccgt

     S. cerevisiae  atgtacaccgtattggtggaacatcactgccaaattttttatcccattttcacatagttccccttaaaag
            sacPar  atgtccgtcgtattggtagaagatcactgtcata-attttatcccattttcacatagttccccttaaaag
            sacMik  atgttcatcgtattagtatgatatcactatcaaa-ctttcatcccattttcacatagttccccttaaaag
            sacKud  atgttccttgtctttgtagaatactattatcaaa-ttttaatcccatttctacacggttccccttaaagg
            sacBay  atgtctttcgtcttagcagaatcttactatcaag-ttttcatcccatttgtacacggttccccttaaaag

     S. cerevisiae  aaactttgttagtatctttaaccc-tttacactgtgggggtaaaatattac
            sacPar  aaactttgttagtatctctaaccc-tttacgctgtgggggtaaaatattac
            sacMik  aaactttgctagcatctttaaccc-tttatactgtgggggtaaaatattac
            sacKud  aaactttattggcatctttaaccc-tttgtgctgtgggggtaaaatattac
            sacBay  aaagtttattcatatctttaacccttttatgctgtgggggtgaaataatac

Alignment block 6 of 9 in window, 195702 - 195754, 53 bps 
B D  S. cerevisiae  cgcttcggagatttctttgacag-gggagcagggaaa-aagcgatgagtgaaaga
            sacPar  cgcttcggagatttctctgacaa-gggcgcagggaaa-aagcgatgagtaaaagc
            sacMik  cgcttcggagatttctctgtcaa-gggagcagagaaa------------------
            sacKud  cgcttcggagatttctctgtcaa-gaaaactgagaaaaaagcgatgagttagaag
            sacBay  cgcttcggagatttctctgtaag-ggaagcagaaaagaaagcgatgagtggcagg
            sacKlu  tgactagaagatagcttttacaacgggaacaagactaagagcgttagataaaaca

Alignment block 7 of 9 in window, 195755 - 195877, 123 bps 
B D  S. cerevisiae  a-agggaa--tgc--gatgataaagatgataa------tgttgcaaacggtgagaaacttgcagatcgca
            sacPar  a-aggaaa--tgctggacgataaagatgatct------tgatccaaacagtgggagaattgtagtttgta
            sacMik  ------ag--tgc--gataataaagatgataa---tagtggtgcaaactgagggaggctaatagatcgta
            sacKud  c-ggtaaacgtgc--aacgacgtacgtgtcaa---tcgcggtgcaaacagcgaaaagtcagtagcttaca
            sacBay  cggggaaa--tgc--acagtgacagttaatgaagaaagtggtgcagatgatgaaaggctcatatcttg--

     S. cerevisiae  gtggctaattctta-atctttatattttaacaagacttctaaa-------cgt-aaaccgcagattgctg
            sacPar  gtagccaagtgctatatttttatatttttagaaagccttttaa-------tat-aaactgcgaattgctg
            sacMik  gcg---aagtgttatatctgtat-ttgtagagaggcttgtaagtataaactgt-aaactgtaaactgctg
            sacKud  gtagttggctattc-atttg-gtatttttaaaagcatattaag-------tacaaaactgcggattgctg
            sacBay  -------------acgtctgttt-gtttatagaggcatgtaaa-------taaaaaacaatgaattgcta

     S. cerevisiae  cat
            sacPar  cgt
            sacMik  cat
            sacKud  cat
            sacBay  cct

Alignment block 8 of 9 in window, 195878 - 195918, 41 bps 
B D  S. cerevisiae  acatacaaggatacacacacacagacggaca------------ctaaacatct
            sacPar  atatacaaggatacacaaacacacacacacatacatacacgccctacacatat
            sacMik  atatataggtataaacagctataga--gacg----------------------
            sacKud  atatacatggagacaaacatacatacatata----------------------
            sacBay  gcctaca------------tatatacatata----------------------
            sacCas  acaaataacaaaacataacaaaata---aca------------ttttagatat

Alignment block 9 of 9 in window, 195919 - 196097, 179 bps 
B D  S. cerevisiae  ac----gtacatacatatacatatatacataat----------gtttaacgtgattggtgggggacgtta
            sacPar  ac----gtacatatatacacacatatatat--t----------gtctaacgtgattggtgggggacgtta
            sacMik  ------------------gtatatatacac--t----------gtttagcgtgattggtggggaacgtta
            sacKud  -----------tacatacatacagacagat--t----------atttaacgcgattggtggggaacgtta
            sacBay  -----------------tatatatatgtat--c----------gtttaacgagattggtggggaacgtta
            sacCas  aca---gtatatatatgtaggagtgtatat--tacaacgaggggcttagcgcacctggtggggcacgttt
            sacKlu  --aaaaaaaaaaaaaaaaaaaaatagaaat--t----------gtctagcggaattggcgtggtacattg

     S. cerevisiae  ccacatctatccttgccaaagtttattttgagatctttgaaataggggttagacttaatcttgtctaagg
            sacPar  ccgcatctatctttgccaaaatttattttgagatctttgaaataggggtttgacttaatcttgtctaagg
            sacMik  ccgcatctatctttgccaaagtttattttaagatctttgaaataggggttcgatttaattttgtctaagg
            sacKud  ccgcacctatctttgccaaaattgattttgagatctttgaaatacggatttgacttgatcttgtctaaag
            sacBay  ccgcacctgtctttaccaaaattgatcttgaggtctttgaaatatgggttggacttgatcttgtctaaag
            sacCas  ccacatctgtccttcccgaagttgatcttcaggtcctcaaagtgagggttggacttgatcttgtctagcg
            sacKlu  ccacatctatctttgccgaaattaaccttgagatttttgaagtaaggattacacttgatcttgtcgatgg

     S. cerevisiae  ctaaaatagcattactgatgttagtataattgatgaaacaacagttcttctca
            sacPar  ctaaaatagcattactgatgttagtataattgatgaaacaacagttcttttca
            sacMik  ccaaaatagcgttactaatgtttgtatagttaacgaaacaacagttcttttcg
            sacKud  ctagtatagcgttactgatgttagtataattaatgaaacagcagttcttctca
            sacBay  ccaaaatagcattactgatattggtataattaataaagcaacagtttttctca
            sacCas  ccaaaatggcattgctgatgttggtgaaattgataaagcaacagttcttttct
            sacKlu  ccaatatagcgttgctgatgttagtgaagttgataaagcaacagtttttttca

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Go to Conservation track controls

Data last updated at UCSC: 2011-09-01

Description

This track shows a measure of evolutionary conservation in seven species of the genus Saccharomyces based on a phylogenetic hidden Markov model (phastCons). The graphic display shows the alignment projected onto S. cerevisiae.

The genomes were downloaded from:

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Pairwise alignments of each species to the S. cerevisiae genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults). Note that excluding species from the pairwise display does not alter the the conservation score display.

To view detailed information about the alignments at a specific position, zoom the display in to 30,000 bases or fewer, then click on the alignment.

Gap Annotation

The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used:

  • Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the S. cerevisiae genome or a lineage-specific deletion between the aligned blocks in the aligning species.
  • Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.
  • Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Downloads for data in this track are available:

Base Level

When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the S. cerevisiae sequence at those alignment positions relative to the longest non-S. cerevisiae sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".

Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:

  • No codon translation: The gene annotation is not used; the bases are displayed without translation.
  • Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment.
  • Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding.
  • Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation.

Gene TrackSpecies
SGD GenesS. cerevisae
No annotationall the other yeast strains
Table 2. Gene tracks used for codon translation.

Methods

Best-in-genome pairwise alignments were generated for each species using lastz, followed by chaining and netting. The pairwise alignments were then multiply aligned using multiz, and the resulting multiple alignments were assigned conservation scores by phastCons.

The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Note that, unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size, so short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. (2005).

PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.

Credits

This track was created at UCSC using the following programs:

  • Lastz (formerly Blastz) and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group.
  • AxtBest, axtChain, chainNet, netSyntenic, and netClass by Jim Kent at UCSC.
  • PhastCons by Adam Siepel at Cornell University.
  • "Wiggle track" plotting software by Hiram Clawson at UCSC.

The phylogenetic tree is based on the Saccharomyces Phylogeny page from the Department of Genetics at Washington University in St. Louis.

References

Phylo-HMMs and phastCons:

Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351.

Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396

Chain/Net:

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Multiz:

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317

Lastz (formerly Blastz):

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.