Publications - Supplemental material

Please find below supplemental material corresponding to publications of our group. Currently, we list 133 supplements. If you have problems accessing electronic information, please let us know:

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This supplement is also available at http://www.bioinf.uni-leipzig.de/publications/supplements/03-007
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BIOINF 03-007: Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution

C-H. Chiu, Ken Dewar, Günter P. Wagner, Kazuhiko Takahashi, Frank Ruddle, Christina Ledje, Peter Bartsch, Jean-Luc Scemama, Edmund Stellwag, Claudia Fried, Sonja J. Prohaska, Peter F. Stadler, Chris T. Amemiya

The Complete HOXA Cluster Sequence of a Primitive Ray-Finned Fish Provides Insights into the Duplication and Evolution of HOX Clusters Within the Bony Fish Lineage


C-H. Chiu, Ken Dewar, Günter P. Wagner, Kazuhiko Takahashi, Frank Ruddle, Christina Ledje, Peter Bartsch, Jean-Luc Scemama, Edmund Stellwag, Claudia Fried, Sonja J. Prohaska, Peter F. Stadler, Chris T. Amemiya

  • Supplement 1:
    BAC Library Construction (html document)
    [Printable PDF document]

  • Supplement 2:
    BAC Library Screen (html document)
    [Printable PDF document]

  • Electronic only Supplement 2a: Sequences
    Polypterus senegalus Hox-A cluster [FASTA format]
    Takifugu rubripes Hox-Aa cluster [FASTA format] Takifugu rubripes Hox-Ab cluster [FASTA format]

    For comparison see also: Annotation of the HoxA clusters by Shawn Hoon:
    Distribution of Non-Coding Region alignments of HOX A clusters

  • Supplement 3:
    Remnants of the HoxA7 gene
    in Bichir and Fugu (html document)
    [Printable PDF document]

  • Supplement 4: Hox Protein Alignment
    [Printable PDF document]
    Individual alignment files of Hox proteins:
    HoxA2 [full alignment] [MacClade characters only]
    HoxA6 [full alignment] [MacClade characters only]
    HoxA10 [full alignment] [MacClade characters only]
    HoxA11 [full alignment] [MacClade characters only]
    HoxA13 [full alignment] [MacClade characters only]

  • Supplement 5:
    Footprint Analysis
    [Printable PDF document]

  • Electronic-only Supplement 5a:
    Table of alignments of all co-linear cliques found by tracker.
    [Text & Figures]

  • Supplement 6: PFCs from Chiu et al. (2002)
    [Printable PDF document]
    Also available as individual htlm documents:
  • Heterodontus francisci A (html)  [xls]
  • Homo sapiens A (html)  [xls]
  • Danio rerio Aa cluster (html)  [xls]
  • Morone saxatilis Aa cluster (html)  [xls]
  • Danio rerio Ab cluster (html)  [xls]

    • Correspondence regarding the paper should be addressed to Chi-hua Chiu at Chiu@nel-exchange.Rutgers.Edu.
    Problems with the webpages themselves should be reported to Jens Steuck,