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Vectorbase probe mapping

Vectorbase probe mapping. Automati c Annotation. Automati c Annotation. Array data. browser. Manual Annotation. CHADO. XML. browser. vectorbase. Contigview View alignment track Geneview Reporters experiments Expression patterns?. Reporter page Positions mapped

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Vectorbase probe mapping

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  1. Vectorbase probe mapping

  2. Automatic Annotation Automatic Annotation Array data browser Manual Annotation CHADO XML browser vectorbase

  3. Contigview View alignment track Geneview Reporters experiments Expression patterns? Reporter page Positions mapped Genes overlapped Experiments used in Integration aims

  4. Linked to location: • Feature track • Link to BASE • Detail popup: • st-end, name, %id… contigview

  5. Associated with gene: • Reporter • Experiments(?) geneview

  6. Slow Delayed data flow Limited scope for adaptation a load of links… DAS Vs. e!

  7. DAS - request:response DB server DAS browser request

  8. data flow Automatic Annotation Array data Manual Annotation CHADO 2 3 XML 4 DAS browser browser 1 2 3 name chr::start-end::strand

  9. Slow Delayed data flow Limited scope for adaptation a load of links… Fast Data generated with new assembly Fully integrated with ensembl Pages are extendable & adaptable DAS Vs. e!

  10. affy feature cf affy_feature

  11. featureview

  12. ContigView display track FeatureView positions in genome FeatureView positions in genome other features est is associated with DNA_Align_Feature Is feature associated with any external databases? (i.e. EMBL) GeneView display information with associated gene Xref est sequences > 97% identity > 90% coverage e! features

  13. Already handled by ensembl • MMC1 • Spotted array: cDNA clones • MMC2 • Spotted array: PCR products • Affy • Short oligo tiling path • Agilent • Long oligo, tiling path? probe types

  14. MMC1 (clones) exonerate: EST2genes ContigView display all features in ‘probes’ track DNA_Align_Feature (ESTs) FeatureView: positions in genome collapse ESTs into clones Misc_Feature (REPORTER) 1 - est2reporter

  15. est1 2L len (est2)+len (est1) est2 est2 500 + 300 = 800 len est2 est2 est2 500 = 500 est1 300bp est2 500bp 3R 2 - est2reporter

  16. 3 - est2reporter len (est2)+len (est1) 500 + 50 = 550 len est2 500 = 500 est1 50bp est2 500bp est1 2L est2 est2 est2 3R est2 est2 est2

  17. MMC1 (clones) exonerate: EST2genes MMC2 (primers) e-PCR ContigView display all features in ‘probes’ track DNA_Align_Feature (ESTs) Marker_Feature (PCR primers) FeatureView: positions in genome collapse ESTs into clones assess significance? Misc_Feature (REPORTER) pcr2reporter

  18. sts pipeline 550bp => map weight 0 100bp => map weight 1 800bp => map weight 1 2L 3R

  19. 1 - reporter2gene ENSANG00012345: MMC1: 4A3B-AAG-D08 MMC2: 9713 2L

  20. MMC1 (clones) exonerate: EST2genes MMC2 (primers) e-PCR ContigView display all features in ‘probes’ track DNA_Align_Feature (ESTs) Marker_Feature (PCR primers) FeatureView: positions in genome FeatureView: positions in genome Links to genes Links to experiments collapse ESTs into clones assess significance? Misc_Feature (REPORTER) GeneView display reporters (& experiments?) in geneview Xref: criteria? % alignment overlap w. exon boundaries Xref 2 - reporter2gene

  21. MMC1 locations

  22. MMC1 locations table

  23. MMC1 genes

  24. MMC1 genes table

  25. MMC2 locations

  26. MMC2 genes

  27. MMC2 table

  28. MMC DAS tracks http://base.vectorbase.org:8080/das

  29. http://base.vectorbase.org:8080/MMC1.jsp http://base.vectorbase.org:8080/MMC2.jsp MMC listings

  30. Thanks… Bob, George, Fotis Dan, Karyn, Martin @ EBI Ian Sealy @ Sanger Informatics support @ Sanger fin

  31. TOTAL: 19280 • OK: 17186 (89.14%) • POOR: 2094 (10.86%) • repetitive: 2094 • short: 36 • avg length (bp): 576.39 • avg repeat %: 1.05% EST quality

  32. process object run executable Exonerate DB record >> perl object e! DB runnable runnableDB BLAT get object from db ePCR perl object >> DB record general runnable

  33. Exonerate DB record >> dna align object e! DB runnable runnableDB BLAT MMC1_xref reporter XREF ePCR dna align object >> DB record MMC1 runnable

  34. Exonerate DB record >> marker object e! DB runnable runnableDB BLAT MMC2_xref reporter XREF ePCR marker object >> DB record MMC2 runnable

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