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Scott Zuyderduyn 05 Feb 2004 MEDG505

Assessing the Drosophila melanogaster and Anopheles gambiae Genome Annotations Using Genome-Wide Sequence Comparisons. Jaillon O, Dossat C, Eckenberg R, Eiglmeier K, Segurens B, Aury J, Roth CW, Scarpelli C, Brey PT, Weissenbach J, Wincker P

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Scott Zuyderduyn 05 Feb 2004 MEDG505

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  1. Assessing the Drosophila melanogaster and Anopheles gambiae Genome Annotations Using Genome-Wide Sequence Comparisons Jaillon O, Dossat C, Eckenberg R, Eiglmeier K, Segurens B, Aury J, Roth CW, Scarpelli C, Brey PT, Weissenbach J, Wincker P Genoscope/Centre National de SequencageUnite de Biochimie et Biologie Moleculaire des Insectes, Institut Pasteur Genome Res. (2003) 13:1595-99 Scott Zuyderduyn05 Feb 2004MEDG505

  2. Genome Sequences Drosophila melanogaster“Fruit Fly”Sequenced by Celera Genomics (Myers EW et al., 2000) Anopheles gambiae“Malaria Mosquito”Sequenced by Celera Genomics (Holt RA et al., 2002) BACKGROUND

  3. Genome Comparisons BACKGROUND 1. EnsEMBL (http://www.ensembl.org)2. Zdobnov EM et al. (2002) Science 298:149-159.

  4. Exofish EXOn FInding by Sequence Homology (+)(-)Ecores BDGP release 2 (+)(-)Ecores BDGP release 3 RESULTS

  5. Ecores in Drosophila RESULTS

  6. New Annotations EnsEMBL Anopheles gene predictions (+)(-)EcorescDNA RESULTS

  7. Annotating Anopheles with Drosophila EnsEMBL Anopheles gene prediction (+)EcorescDNA homolog of Innexin-7 RESULTS

  8. Refining Annotations EnsEMBL Anopheles gene prediction (+)EcorescDNA RESULTS homolog of tetraspanin family member

  9. Ecores in Anopheles RESULTS

  10. Themes • An annotated genome can be used to start annotation of a new genome • An existing genome can be used to assess the annotation/assembly progress of a new genome • A new genome can be used to refine annotations of the existing genome CONCLUSIONS

  11. Questions • How evolutionarily distant do two organisms have to be in order for their genomes to be effective in annotating coding regions? regulatory elements? • Are there alternatives to sequence-based (primary structure) comparisons? • Comparative genomic approaches make inferences from common elements. What about novel elements? • In comparative genomics, the more genomes the better: what types of knowledge are gained as we include more genomes? CONCLUSIONS

  12. Comparative Genomics BACKGROUND Zdobnov EM et al. (2002) Science 298:149-159.

  13. Fly-Mosquito Comparative Genomics BACKGROUND

  14. Exofish EXOn FInding by Sequence Homology • Used the well-characterized Drosophila ADH region and a set of Anopheles shotgun sequence reads to optimize TBLASTX parameters RESULTS

  15. RESULTS Comparative Genoscope (http://www.genoscope.cns.fr/comparative)

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