Publications - Supplemental material

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BIOINF 09-002: Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome

Chris T. Amemiya, Thomas P. Powers, Sonja J. Prohaska, Jane Grimwood, Jeremy Schmutz, Mark Dickson, Tsutomu Miyake, Michael A. Schoenborn, Richard M. Myers, Francis H. Ruddle, Peter F. Stadler

Figures of Main Text

  • Figure 1 [PDF] (6K)
  • Figure 2 [PDF] (9K)
  • Figure 3 [PDF] (6K)
  • Figure 4 [PDF] (6K)
  • Figure 5 [PDF] (15K)
  • PNAS supplemental text [PDF]
  • PNAS supplemental data [PDF]

    • Sequences

  • List of primer oligos
    [PDF]
  • List of clones
    [PDF]
  • Assembly: map of contigs
    [PDF]
  • Assembled Hox cluster sequences and annotations
    Cluster Genbank fasta Annotation Peptides
    HoxA FJ497005 [LmA.fa] [text] [fasta]
    HoxB FJ497006 [LmB.fa] [text] [fasta]
    HoxC FJ497007 [LmC.fa] [text] [fasta]
    HoxD FJ497008 [LmD.fa] [text] [fasta]
  • Comparison of IGR length between human and coelacanth [PDF]

    • Noncoding Sequence Conservation

  • VISTA plots
    mVISTA overview
    individual HOX clusters [PDF]

    VISTA Evx region
    HoxA/HoxD comparison [PDF]

    Comparison of A and D clusters
    Reference: Human HoxA [PDF]
    Reference: Human HoxD [PDF]

  • List of tracker/dialign-2 footprints
    [HoxA] [HoxB] [HoxC] [HoxD]
  • PERL script mAAna_tropy.pl
    source code as an archive [tar]
    README [txt]

    • Repetitive Elements

  • Consensus sequences of tRNA-like repetitive sequences
    [fasta]

    • Relative Rate Tests

  • Relative Rate Tests on protein coding sequences
    Extensive data with alignments: [PDF]
    Short summary: [PDF]

  • CNCN relative rate test
    Outgroups are Heterodontus francisci HOXA and Polypterus senegalusHOXA. Latimeria is tested as variable "foreground" against the assumption of contant rates of both outgroups and the 2nd ingroup (negative z' values mean that Latimeria is slower), and as part of the "background" (positive z' values mean that the 2nd outgroup is faster than outgroups and Latimeria.
    ingroupforegroundbackground
    XtA -3.112 *** 4.939 ***
    GgA -3.687 *** 6.119 ***
    MdA -2.325 ** 3.301 ***
    CfA -1.735 * 2.275 **
    MmA -1.864 * 2.494 **
    RnA -1.840 * 2.449 **
    HsA -1.599 ns. 2.051 **

    p <0.01 *** p <0.05 ** p <0.1 *

    Bootstrapping example

    Distribution of z' values after resampling CNCNs (HfA,PsA,LmA,MdA) in 100 replicates. The triangle give the value of the original data, bullet and whiskers indicate mean man and standard deviation of the bootstrapped distribution.