Lee Apollo Bosc2008
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Lee Apollo Bosc2008

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Lee Apollo Bosc2008 Lee Apollo Bosc2008 Presentation Transcript

  • Apollo: A Sequence Annotation Editor Ed Lee Lawrence Berkeley National Laboratory
  • User Community
  • Workflow
  • Main Window
  • Annotation Info Editor
  • Architecture
  • Data Layer
  • Supported Formats
  • Chado
    • Official relational database schema for GMOD
    • Highly sophisticated
    • http://gmod.org/wiki/index.php/Chado
  • Chado
  • GFF3
    • Generic Feature Format Version 3
    • Extension to previous GFF formats
    • Sequence Ontology compliant
    • Used by many communities
    • http://www.sequenceontology.org/gff3.shtml
    D. melanogaster C. elegans S. cerevisiae Dictyostelium A. thaliana D. rerio M. musculus H. sapiens S. pombe E. coli R. norvegicus
  • GFF3
  • Style Wizard
  • Types Wizard
  • Multiple Alignment Transcript Viewer and Editor
  • Continuous Data Display
  • Undo
  • Future Plans
    • Redesign the data model to reflect the Chado schema
    • Enable communication with analysis servers that provide access to popular sequence analysis tools (e.g., NCBI BLAST, WU-BLAST, ePCR)
    • Integration with GMOD’s GBrowse
  • Downloading Apollo
    • http://apollo.berkeleybop.org
    • Source tarball from SourceForge
    • Source from SourceForge CVS
      • http://gmod.cvs. sourceforge .net/gmod/apollo
    Platform Optionally bundled JRE Windows Yes Mac OS X No Linux Yes Solaris Yes (x86 version) Unix No
  • Acknowledgements
    • Lawrence Berkeley National Laboratory
      • Suzanna Lewis (project PI)
      • Nomi Harris
      • Mark Gibson
    • Wellcome Trust Sanger Institute
      • Steven Searle
    • The Arabidopsis Information Resource
      • Raymond Chetty (new MSA viewer)
    • Apollo community
    • The National Institute of General Medical Sciences (NIGMS) for funding (NIH grant 1R01GM080203-01)