Multiz Alignments of 7 Yeasts
 

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Alignment block 1 of 8 in window, 376757 - 376766, 10 bps 
B D  S. cerevisiae  ttagagggtt
            sacPar  ttaga-gatt
            sacMik  tcagaaagtg
            sacKud  ttataaagtc
            sacBay  ctacaaattt
            sacCas  attgggggtt

Alignment block 2 of 8 in window, 376767 - 376794, 28 bps 
B D  S. cerevisiae  ttgggatgttcatctgatgtaacgacat
            sacPar  tctggatgttcgtctgatgtaacgatgt
            sacMik  tcgggatgttcatctgatgtaactacat
            sacKud  cctgggtgttcatctgatgcgacgacat
            sacBay  ccaggatgttcatctgatgtgatgacgt
            sacCas  tttgtatcttcatgttgggaaatgttat

Alignment block 3 of 8 in window, 376795 - 377823, 1029 bps 
B D  S. cerevisiae  acacgcccttatccttctcttggcatttaaagttcttgttcttcaaatcgttccatttcttatgcggaat
            sacPar  acacgcccttatcattctcctggcatttaaagttctcgttctttaaatcattccattttttatgcggaat
            sacMik  atacacctttatctttctcctggcacttaaatactttgttcttcaggtcattccatcttttatgagcaat
            sacKud  atacacctttatctttctcccggcattcgaatttcttgttctttaaatcattccatttcttgtggggaat
            sacBay  atacccctttatccttttcctgacagtcaaatttcttggttttcaaatcattccattttttatggggaat
            sacCas  aagttcctttctccttttctatacaatcaaagacttcggtttttaatatttcccatttcttgtgtggaat
            sacKlu  acacacccctgtcctgctcctcacacgcaaacgccttgtgctcgagctgggcccatttgtcatggggtat

     S. cerevisiae  cgtccagccacatttttgggctaccatagctgcaatgtcatcacagtaccccaaaagagataaatcaaat
            sacPar  tgtccagccacatttctgagctaccatagccgcaatatcatcgcagtaccccaaaagggacaaatcaaat
            sacMik  tgtccagccacacttctgagctaccatagctgcaatatcatcacaataccccaaaagggataaatcaaat
            sacKud  tgtccaaccacatttctgagcaaccatggctgcaacatcatcacagtaacccaagagggataggtcaaat
            sacBay  tgcccaaccacatccctgtgctaccatagctgcaatatcatcacagtatcccaaaagagatagatcgaat
            sacCas  atcccatcctgatttctgcgctactaatgcagcaacatcatcacaaaatcctaacaggttcaaatcaaac
            sacKlu  ctcccatccgcacttttgggcaaccagcgcggccacgtcgtcacaaaagcccaacagcgagagatcgaac

     S. cerevisiae  tctgcgtgcttgacgggatcacgattaatcaggacttggggaacgtgggaaggaaccatgtttacgattt
            sacPar  tctgcgtgctttaccggatcacggttaatcaggacttggggaacgtgggcagggatcatatttacgattt
            sacMik  tctgcgtgtttgacgggatcacggttaatcagcacctggggaacatgtgcagggaccatatttacaattt
            sacKud  tctgcgtgcttgacggggtcatagttgatcaggacttgaggaacgtgcgcagggaccatatttacgatct
            sacBay  tctgcgtgtttgacaggatcgcggttgattaagacctggggcacgtgcgctgggatcatatttacaatct
            sacCas  tcagcatgtctcacaggatctctattaattagtacttgtggtacatgtgcgggaaccatattcacaattt
            sacKlu  tcggcgtgttttactgggtccttgttgatcaacacctgtggaacgttcgcaggaaccatgttgacgattt

     S. cerevisiae  cagacactggcgctacttttaaacttgtcccaatgcaaatcaacaaatcacattctaagatatcttcgcg
            sacPar  cggatactggtgctacttttaaacttgtcccgatgcagatcaacaaatcgcattccaggatatcttcacg
            sacMik  cggatactggtgctacctttaaacttgtcccaatgcaaatcagtaaatcacatttcaaaatatcttctcg
            sacKud  cggatactggtgccactttcaaacttgttccaatgcaaatcaacaaatcacattccaaaatgtcttcacg
            sacBay  cggataccggcgccactttcaaacttgtcccaatgcaaatcaataaatcgcattctaaaatatcttggcg
            sacCas  cagaaacaggtgccacttttaaactggtacctatgcaaatcagtagatcacatttcaaaatatcctcacg
            sacKlu  cggacactggggcaaccttcaaactcgtccctatgcagatcagcaggtcgcacttcaacacgtcctctct

     S. cerevisiae  aatgctcttatgaaatttatttggcagtgcttcgccaaagaatgtgatatctggtttgagaacgccatat
            sacPar  aatactcttgtgaaatttatttggcagagcttcaccaaagaacgtgatatcgggtttgagaacaccgtat
            sacMik  aatgctcttatgaaatttacttggcagagcttccccaaagaaagtgatatcgggtttgagaacgccatat
            sacKud  gatactcttgtggaatttacttggcaaagcctcgccaaaaaacgtgatatctggtttgaggacaccgtat
            sacBay  gatgctcttgtgaaatttgtttggtagagcttctccaaaaaacgtgatatccggttttaggacaccatat
            sacCas  aatggttttatgaaatttagatgggagggcttcaccaaaaaatgtaatatctggttttaagacaccgtac
            sacKlu  gataaaccggtggaacttggagggcaaggcttcgccaaaaaacgtgatgtctggcttcagaacgccgtag

     S. cerevisiae  gagttaag-------------gatat-----atggag------------------------gccttt--c
            sacPar  gagttgag-------------gatat-----atggag------------------------gccttt--c
            sacMik  gagttgag-------------aatat-----atggag------------------------gccttt--c
            sacKud  gagttgag-------------gatat-----atggag------------------------gtcttg--t
            sacBay  gagtttag-------------tatat-----acgagg------------------------gctttg--c
            sacCas  gattttagtgcttgtcctgtaaattt-----accgct------------------------gtttttcgc
            sacKlu  gacttcat-------------catgtggaacacagagtttgggttgctggcagcggaaggagccttg--a

     S. cerevisiae  cgacattgaa----ccctgtgatgcagcaacacctact-------------------------ttat---
            sacPar  cggtgctgaa----acctgagatgcagcgacttctact-------------------------ttattag
            sacMik  tgaagtagaa----gtcagagatgcagaactatctact-------------------------ctat---
            sacKud  cggagccgaa----tcttgtgaagatgtaccgtccaat-------------------------ctgttgg
            sacBay  tagggcagaa----tcttgcatcgctctcccattgatc-------------------------ttattgg
            sacCas  caatgttgga----------------------tctaat-------------------------ttag---
            sacKlu  cggcaccgagaccgcccgctgctgctgccgctgctaccgccgccgccgccgccgccgtcgtcgtcgtcgc

     S. cerevisiae  ------------tattatatccc-----------tctgggaaatattctcttctttttttgtaacagtac
            sacPar  aatttgaagtactattatatcct-----------tccgggaaatactctcttctttttttatagcagtac
            sacMik  ---tggaagtgctgttgtatccc-----------tctggaaaatattctcttctttttttataacagtac
            sacKud  agttagatggactgttgtacccc-----------tctgggaaatactctcttctttttttaaagcaatac
            sacBay  aattggaaatactgttatatcct-----------tctggaaagtactctctccttttcttgtaacaatac
            sacCas  ------------cattat---ca-----------ttgggaaaatattctctccttttcttataacagtat
            sacKlu  cacagcggttcccgccacatcctggtcggtggtggtcgggtactggtccttgcgcttctggtagcagtag

     S. cerevisiae  gggcatagtggaagttcgaggtttctaattttattaaatatcctctcaccgggtaggttccaatggcagg
            sacPar  gggcataatggaagttcgaggttcctaattttattaaatattctctcaccgggtaggttccaatggcaag
            sacMik  gggcataacggaagttcgagatttctaattttattaaatattctctcgccaggtaggttccaatggcaag
            sacKud  gggcatagtggaagttcaaggttcctgattttattgaatatcctctcgccaggtagattccaatgacaag
            sacBay  gggcataatggaagctcgaggtttctaattttattgaatattctctcgcccggtaggttccaatgacaag
            sacCas  ggacataatggtaattccattttccttatattctcaaagattttttcaccaggtaatttccaatgacaag
            sacKlu  gggcacaagggcaactccagcctccttatgttcccaaagatcttctcgccgggtagcttccagtggcagg

     S. cerevisiae  taacgcaggtggcagtagcaaaagagccatggcactgcaccagtttatctgtgcttattcccgcataaga
            sacPar  taacacaggtggcagtagcaaaagagccatggcactggaccagtttatctgtgcttattccagcataaga
            sacMik  taacgcatgttgcagtagcaaaagagccatgacattggaccaatctatccgtgcttattcccgcgtaaga
            sacKud  taacgcatgtggcagtagcaaaagaaccgtggcactgaactaatttatcagcgcttattccagcatagga
            sacBay  taacacacgtggcagtggcaaaagagccatgacattggaccaatttatcattgtttatacccgcgtaaga
            sacCas  taatacaggatgcagtagcaaaggacccatgacattgtaccaagttttccgccttgataccagcatatga
            sacKlu  tgacacacgatgccgtggcaaacgagccgtggcactgtaccatcttctcggcctggatgcccgcatagga

     S. cerevisiae  ttccaaattatcaatgttttgagtataatttctcaataatttccctttcatttgtagcatcttaatgaaa
            sacPar  ttccaaattatcaatgttttgagtataattcctcaataacttcccttttgtttgtagcatcttaatgaaa
            sacMik  ttccaaattatcaatattttgagtataatttctcaataacttccctttcgtttgtagcatcttgatgaag
            sacKud  ttctaaattgtcaatgttttgagtataattcctcaataatttaccctttgcttgtaacatcttaataaag
            sacBay  ttccaagttgtcaatgttttgagtgtaattcctcagtagtttcccttttgtttgtagcatcttaataaag
            sacCas  ctctaaattatcaatattttgtgtgtaattcctcaacaacttccccttatcttgaagcatcttaatgaaa
            sacKlu  ctccaggttgtcgatgttctgggtgtagtttcttagcagcttgcccttgtcctggatcatcctgataaaa

     S. cerevisiae  ctatgcaatggagaataaattttttctggaggtaaaaccatattggcaatattatagaaaacagaggggt
            sacPar  ctatgcaatggagaataaatgttttctggcggtaaaaccatatttgcaatattatagaaaacagaaggat
            sacMik  ctgtgcaatggagaataaacattttccggaggtagaaccatatttgcaatattatagaaaatagaaggat
            sacKud  ctatgcaatggagaataaatgttttccggaggtagaaccatattggcgatattataaaaaacggaaggat
            sacBay  ctgtgtaagggagaataaatgttttctggagggagaaccatatttgcaatgttgtaaaacacggaagggt
            sacCas  ctatgcaagggagagtagatgttatctggtggtaaaatcatgtgggaaatattatagaacacagacggat
            sacKlu  ctgtgcaggggggagtacaagttctccggaggcaggaccatgtgcgcaatgttgtagaacacagaggggt

     S. cerevisiae  cgtgcataaatatattgtaattgaaaacgtcttggggatcatcgagccccaaatgtttgatctttgaata
            sacPar  cgtgcataaatatattgtaattgaaaacgtcctgaggatcatcgagccccaaatgcctgatctttgaata
            sacMik  cgtgcatgaagatattgtaattgaagacgtcttgaggatcatcgagtcctaaatgtctaatttttgaata
            sacKud  cgtgcataaaaatattataattgaaaacatcctgaggatcgtcgagccccaaatgtctgattcttgaata
            sacBay  catgcataaatatattatagttgaaaacatcttgtggatcatcgagccccagatgtctgattttcgaata
            sacCas  tctgcataaatatatcgtagttgaaaacatcttgcggatcgtcaaggcctaaatgtttaattttggagta
            sacKlu  cctgcatgaaaatgtcgtagttgaaaacgtcttgcggatcatccaggcccaggtgcttgatcttggagta

     S. cerevisiae  gaacccctcagaagatctgaagtccgggatccctaatgaagttgaaacacctgcaccagtcaggaccaaa
            sacPar  gaacccttcagaagatctaaagtcagggatccctaatgaagttgaaacacctgcaccagtcaggaccaaa
            sacMik  gaatccttcagatgacctaaagtcagggattcctaatgaagtagaaacgccagcgccagtcaacactaaa
            sacKud  aaacccttcagaggatctgaagtcagggattcctaacgaagttgaaactcctgcacctgtcaggaccaaa
            sacBay  gaacccttcagaagatctaaagtcagggatccccaatgaagtagaaacacctgcacctgtcaggaccaaa
            sacCas  aaacccttctgatgatctaaaatcaggtatacccaaagatgtggaaacacctgcccctgtaaggaccaaa
            sacKlu  gaagccctcggaggacctaaagtccgggatgcccagggaggtggagatgcccgcaccggtcaacaccagc

     S. cerevisiae  atttttctagcggtatgtaatttttgaataaaatgatcaatagtgaaaaaattggataatcttaatcttg
            sacPar  atttttttagcggtatgtaatttttgaataaaatgatcaatggtgaaaaaattggataatcttaatcttg
            sacMik  atttttctggcagaatgtaatttttggataaaatgatcaattgtgaaaaaattggacaatcttaaccttg
            sacKud  attttttgagcggtatgtaatttttgaacaaaatgatcgacagtgaaaaaattggataacctcaatcttg
            sacBay  attcttttagcggtatgtaatttttgaataaaatgatcaatagtgaaaaaattggacaatctcaatcttg
            sacCas  attctatttgctgtcttcaacttatcgacaaaatgttcaatagtataaaaattcgataaccttaatcttg
            sacKlu  actcgcctggccgtcttgagcttggcggcaaagtgctccagagtgtggaagttggccagctttatgcgcg

     S. cerevisiae  tacatagaactttgttaattgctctttgcaaatctttgattagacgaactgtttgcttttttgccaatgg
            sacPar  tacacaaaaccttgttaatcgccctttgtaaatctttgattagacgaactgtttgcttttttgccaacgg
            sacMik  tacataaaaccttgttaattgctctctgtaaatctttgattaaacggactgtttgcttcctcgccaacgg
            sacKud  tgcatagaaccttattgattgctctttgtaaatctttgattagacgaactgtttgtttctttgccaacgg
            sacBay  tacataagactttattaatggctctttgtaaatctttgattaaacggactgtttgcttttttgctagagg
            sacCas  tgcaaagaactttattgatagccttttgtaaatctttaatgagacgaactgcctgcttcttctctagagg
            sacKlu  tgctgagcaccttgttcatggccttttgaaggtccttgatcaggcgcacggcgtgcctcttttcgagcgg

     S. cerevisiae  gtcttcaa
            sacPar  gtcttcca
            sacMik  ctcttcca
            sacKud  gtcttcta
            sacBay  atcttcca
            sacCas  atcct---
            sacKlu  gtcgtcaa

Alignment block 4 of 8 in window, 377824 - 378109, 286 bps 
B D  S. cerevisiae  catttgtgacagatattgcacttcccaa---------atcttgaacacgc---tcttgcgagttga---t
            sacPar  cacttgtaacagaaattgtactttccaa---------atcttggaggggc---tctggcgggttta---t
            sacMik  tatttataaccgatactgttctttctag---------atcctgaaggtgt---tctggcggagtta---t
            sacKud  cattggtaacagatatcgtatttttcga---------atcctgtggatgc---tcgggtgggctta---t
            sacBay  cattggtagcggatactgtattttccga---------atcctgtatatgc---tccggagtgcttg---t
            sacCas  ---------cgtattcaattctttccaatgactcattgtcatctatatgcatatctggatcgatgaattc

     S. cerevisiae  atggacaatactgttgatggtgccgataagcgcttgatctttaacttcaaagcctagcaacttgataaga
            sacPar  atgaacaatactgttgatggtgccgataagcgcttgatccttgacttcaaagcctagcaacttaatcaga
            sacMik  atgaacgatactattgatggtgcctataagcgcttggtccttaacctcaaaacctagtaacttgatcaga
            sacKud  atgaacaatactgttgatagtgccgataagcgcttgatccttgacttcaaaacctagtaatttgattaga
            sacBay  atgaactatactgttgatgttgcttattagggcttgatctttgacttcaaaacccagcaacttgatcaaa
            sacCas  ataaacaacatt-----------taataaat-cacgatcttttatttcaaaccctagtaatttgattaaa

     S. cerevisiae  tagtaaatgtataacgagttcaaatcctcggggaggtaagtgtctaaaaatttgtgtgcaccatagtatt
            sacPar  tagtatatatataacgagttcaaatcctcggggaggtaggtgtctagaaatctgtgtgcaccataatatt
            sacMik  tagtaaatatataacgagtttaaattctcgggaagataggtgtctagaaacctatgtgcaccatagtatt
            sacKud  tagtaaatgtataacgaattcaaattttcggggagataggtgtctagaaatttatgtgcgccgtaatact
            sacBay  tagtaaacgtataaagagttcaactcttcgggtaaataagtgtctaagaattcatgtgcaccgtagtatt
            sacCas  aaataaatgtatagtgaatttaattcctctggtaaaaatgaatctaaaaaactctttaatccatagtatt

     S. cerevisiae  tcagaaacattcgagcattgagagactctcgtttagtgaaggagggaccatagaaaataccatttgat--
            sacPar  tcaggaacattcgagcatttaaagactctcgtttagtgaaggatggtccgtaaaaaacgccacttgat--
            sacMik  ttagaaacatccgagcatttacagactctcgtttagtgaaggacggcccatagaaaactccacttgat--
            sacKud  ttagaaacattcgagcattaagagactcccctttagaaaaagaaggtccataaaaaatgccacttaaa--
            sacBay  ttagaaacattcgagcgttcagtgactctcgtttagtaaaggacggtccatagaaaatgccgttcgac--
            sacCas  taagaaacattcgggcattcaacgagtcctctttattaattttgggta---agatatatttacctgattc

     S. cerevisiae  -gggtttttactgattatgattgg
            sacPar  -gagtttttactgattataattgg
            sacMik  -gagttcttgctaataacgattgg
            sacKud  -gtattcttaccaattataatcgg
            sacBay  -atgtttttaccaattattattgg
            sacCas  agggtctttactcagaataattgg

Alignment block 5 of 8 in window, 378110 - 378133, 24 bps 
B D  S. cerevisiae  ccccttgggcgtctctggtttcaa
            sacPar  ccccttgggcgtctccggcttcaa
            sacMik  gcccttgggtgtctccggtttcaa
            sacKud  ccctttgggtgtttctggcttcaa
            sacBay  cccttggggtgtttccggtttcaa
            sacCas  tttctttggcggtattggtcttaa

Alignment block 6 of 8 in window, 378134 - 378289, 156 bps 
B D  S. cerevisiae  aacgtcattggacattgacactactgaagctgctgacactgccaagggatccatgtcattagttggtttg
            sacPar  aacgtcattagacatcgacgctactgaagctgctgacactgccaagggatccatgtcattggctggttta
            sacMik  gacgtcatttgacattgacactacagaagctgttgatactgctaagggatccataccactagctggttta
            sacKud  aacgtcattggacattgacactactgaagctgctgacactgttaccggatccatgtcatcagccggtcta
            sacBay  aacctcattagacattgacgctgctgacgctgctgacactgctgtggggtccatgtcgctagccggttta

     S. cerevisiae  agctccatcgatgccacttctccgagcgcagctttagtgtgcccaagtggatctgttgtgttggtttccc
            sacPar  agctccattgatgccacttctccaagcgcagccttagtgtgcccaagcctatttgttatcttggtttcca
            sacMik  agctccatcgaggccacttctttcagtgcggccttagtgtatccaggcttatccgttgtattattttccg
            sacKud  agttgtaatgatgctacgtcctctagcgcagcctgagtgcgttcatgcttgtcagtcgttttaggtttca
            sacBay  agctccattgatgctacctgcccgactgccgcctgagtgtattctttattgtcagccttattggattcca

     S. cerevisiae  tcaaggaatccggctg
            sacPar  tcaaggaagccggctg
            sacMik  taaacaaagctggttg
            sacKud  tcaaggaattggggtg
            sacBay  tcgagaaacccgcctg

Alignment block 7 of 8 in window, 378290 - 378441, 152 bps 
B D  S. cerevisiae  tgctacttttatcttcttatgtgaaggttcatcattatttataatgtcatcgggttgttttctgatcgcg
            sacPar  tgctacttttgacttcttatgcaaaggttcactattatttatagtgtcatcgggttgttttctgatcgcg
            sacMik  tactatttttggcttcttatgcgaaggttctccattatttataatgtcatcgggctgttttctaatcgcg
            sacKud  ggacgcttttggctttttatgcgaagacagttcattaactatattgtcatcgggttgtttcctgatcccg

     S. cerevisiae  tctttatcttgtgtggggcttactgtatttgaaaccttattttcgctagtctttgatacggcgtatttca
            sacPar  tctttatcttgtgtggggcttactgtatttgaaaccttattttcactagtcttcgatacggcgtgattca
            sacMik  ttttgatcttgcgtggagcttactgtatttgaaaccttattttcagtagtcttcgatacagcgtgattca
            sacKud  tttcgatcttgcgtggggcatattgcacttgaaaccttatttttagcattcttcgatacggcgtgattca

     S. cerevisiae  tatgtgggatgg
            sacPar  tatgtgagatgg
            sacMik  tatgtgggatgg
            sacKud  tatgagggatgg

Alignment block 8 of 8 in window, 378442 - 378445, 4 bps 
B D  S. cerevisiae  tcat
            sacPar  tcat
            sacMik  tcat
            sacKud  tcat
            sacBay  tcat

View table schema

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.