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The Apollo Genome Annotation and Curation Tool

The Apollo Genome Annotation and Curation Tool. Nomi L. Harris ( nomi@fruitfly.org ), Suzanna Lewis, Mark Gibson, Colin Weil, John Richter Berkeley Drosophila Genome Project Stephen Searle, Michele Clamp Ensembl Project, Sanger Institute Bioinformatics Open Source Conference (BOSC2002)

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The Apollo Genome Annotation and Curation Tool

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  1. The Apollo Genome Annotation and Curation Tool Nomi L. Harris (nomi@fruitfly.org), Suzanna Lewis, Mark Gibson, Colin Weil, John Richter Berkeley Drosophila Genome Project Stephen Searle, Michele Clamp Ensembl Project, Sanger Institute Bioinformatics Open Source Conference (BOSC2002) August 2, 2002

  2. What is Apollo? • Open source tool for viewing and making annotations on genomic sequence • Annotation editor for GMOD • Gbrowse provides simpler way to view (but not edit) annotations • Apollo lets human experts (biologists) create and refine annotations • Developed by FlyBase-BDGP and Ensembl • Ensembl: standalone human annotation browser • BDGP: Drosophila annotation editor

  3. Advantages • Integrate large amounts of data in visually efficient manner • Browser and editor • Customizable • Open Source, extensible • Multi-platform (Java) • Install from Web or CD

  4. Installer

  5. Loading annotation data • Where do you want to go? • Data source (Drosophila, Ensembl human, etc.) • Chromosome arm, start, end • Cytological band • Gene • Sequence • Filename or URL • Transparent access to GadFly annotation database via CGI • Navigation bar

  6. Main display

  7. How much detail? • Show/hide data types • Change score cutoffs • Expand/collapse tiers • Text info detail panels • IDs hyperlinked to Web pages • Semantic zooming • Start/stop codons • Sequence

  8. Sequence • Zoom in to see bases • Annotated genes automatically translated • Color by splice site potential • Translate/save • Find restriction sites • GC content

  9. Many ways to customize • Config file • Background color, 3D rectangles, user annotation colors, etc. • Types panel • Show, hide, set cutoffs • Color chooser • Drag tiers • Define new data types in config file

  10. Curating annotations • Drag-and-drop creation and modification of gene models • Annotation text editor • Exon detail editor

  11. Synteny Viewer • Cross-species comparisons (mouse/human)

  12. Data adapters • Parser -> data models -> display • Existing data adapters • GAME XML • GFF • Ensembl CGI server • DAS • Write your own data adapter! • Extend AbstractDataAdapter class • Display options defined in config file

  13. How other groups are using Apollo • Bristol-Myers Squibb • Launching Apollo from web browser via mime types • GNF • JDBC adapter layer over BioSQL • Biogen • View human genome alignment between public and Biogen internal database • Connected BLAT pipeline to Apollo • HGMP-RC Fugu Genomics group • Displaying annotations on fugu scaffolds

  14. Coming (very) soon • Style preferences per data adapter • Intron editor • Load & layer multiple datasets • Dynamic analysis launch (BLAST, etc.) • DAS adapter (almost works) • GenBank adapter • Can write GenBank but not read

  15. Conclusions • It works: ten biologists used Apollo to annotate 120Mb Drosophila melanogaster genome • User-customizable • Modular and extensible • Continuing to evolve and improve

  16. Acknowledgements • FlyBase-BDGP • Software: Suzanna Lewis, Mark Gibson, Nomi Harris, Colin Weil, Chris Mungall • Biologists: Sima Misra, Jon Tupy, Simon Prochnik, Josh Kaminker, Chris Smith • Ensembl: Steve Searle, Michele Clamp • Howard Hughes Medical Institute/BDGP: John Richter (Apollo and org.bdgp) • Tim

  17. Code available at SourceForge: www.sourceforge.net/gmod Installer available at www.fruitfly.org/annot/apollo/download.html

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