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Maps and Markers

Maps and Markers. Gramene SAB Report Jan 2006. CMap Improvements. Expanded, reorganized and hidden menus New map glyphs Number of features Crop map Magnify map Improved comparative map selection Filtering of features Collapse overlapping features Correspondence aggregation.

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Maps and Markers

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  1. Maps and Markers Gramene SAB ReportJan 2006

  2. CMap Improvements • Expanded, reorganized and hidden menus • New map glyphs • Number of features • Crop map • Magnify map • Improved comparative map selection • Filtering of features • Collapse overlapping features • Correspondence aggregation

  3. CMap: Reorganized menus

  4. CMap: Collapse Features

  5. CMap: Collapse Features

  6. CMap: Filter Features

  7. CMap: Crop/Zoom map

  8. New maps Rice – Gramene IRGSP Assm 2005 Maize – Bins Wheat – Composite 2004 Wheat – Consensus SSR 2004 7 OMAP physical maps 3 Rice Class I SSR maps 15 QTL maps Updated TIGR assembly Gene models BAC end sequence from wild relatives of rice Additional markers and ESTs New & Updated Maps

  9. Marker Database

  10. Marker Search (Users)

  11. Marker Admin Tool (Curators)

  12. Dataflow Through MarkersDB (I) • Gramene-created maps (Genome browser) • Create or update markers in database • Extract marker data • Run through genome pipeline • Update positions in markersDB, Ensembl, CMap

  13. Dataflow Through MarkersDB (II) • Existing maps (non-Gramene generated) • Enter map positions into database • Reconcile features with markers • Marker name, species, type • Create markers if necessary • Output to CMap

  14. MarkersDB Issues • Improved searches • Marker details • Maps • Improved data downloads • Include marker details • Marker accession IDs • Batch loading of marker data • Map load and output scripts • Ensure all mapped features (except QTL and genes) have a corresponding marker • Reconciliation of new markers with existing ones • Continued curation of undefined markers

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