maps and markers gramene sab report jan 2006. cmap improvements expanded, reorganized and hidden...
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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
New & Updated Maps
• 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
Marker Database
Marker Type Markers
AFLP 950
BAC end sequence 676,959
Clone 602,304
EST 2,530,661
EST Cluster 601,935
Gene Primer 19
mRNA 91,074
Primer 34
RAPD 135
RFLP 7,791
SSR 16,835
STS 65
Tos17 18,023
Undefined 823
4,547,608 total
Species Markers
Barley (Hordeum spp.) 535,720
Maize (Zea spp.) 1,089,433
Oat (Avena spp.) 8,215
Rice (Oryza spp.) 1,475,049
Rye (Secale spp.) 13,260
Sorghum (Sorghum spp.) 260,634
Sugarcane (Saccharum spp.) 339,657
Wheat (Triticum spp. + Aegilops spp.)
787,493
Other 38,147
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
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
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