VectorBase Vectorbase probe mapping

VectorBase Automatic Annotation browser Array data CHADO Manual Annotation XML vectorbase Automatic Annotation

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

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

VectorBase Associated with gene: Reporter Experiments(?) geneview

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

VectorBase DAS server DB request browser DAS - request:response

VectorBase Automatic Annotation browser Array data CHADO Manual Annotation XML DAS data flow 23 4 name chr::start-end::strand

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

VectorBase cf affy_feature affy feature

VectorBase featureview

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

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

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

VectorBase 2L 3R est1 est2 len est2 len (est2)+len (est1) est1 est2 300bp 500bp 500 = = est2reporter

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

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

VectorBase 2L 3R 550bp => map weight 0 100bp => map weight 1 800bp => map weight 1 idleft_primerright_primerdistancenameaccessionspecies 1.1.1GATTACAACATCCAGAAGGAGTCGTAGTACTTGAGGACAGCAAG 104 ENSANGG A.gambiae GCCTTTGCCGGGCTGCTTCGGGGGTTTCGAGCAG 497 ENSANGG A.gambiae GATAATTCAGCGCTACACATTACACCGTAATGCTAACATCGAA 146 ENSANGG A.gambiae GATAATTCAGCGCTACACATTACACCGTAATGCTAACATCGAA 146 ENSANGG A.gambiae CAGTGCTACGTGAAGAATGATCCGCTGTCGAGGGAAC 473 ENSANGG A.gambiae 1.1.2TCGTCCAACAGTTTCTCCTACGATCGTTTGCTGCTTGCATA 449 ENSANGG A.gambiae sts pipeline

VectorBase 2L ENSANG : MMC2: 9713 MMC1: 4A3B-AAG-D reporter2gene

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

VectorBase MMC1 locations

VectorBase MMC1 locations table

VectorBase MMC1 genes

VectorBase MMC1 genes table

VectorBase MMC2 locations

VectorBase MMC2 genes

VectorBase MMC2 table

VectorBase MMC DAS tracks

VectorBase MMC listings

VectorBase fin Thanks… – Bob, George, Fotis – Dan, Karyn, EBI – Ian Sanger – Informatics Sanger

VectorBase EST quality TOTAL: OK: 17186(89.14%) POOR: 2094 (10.86%) – repetitive:2094 – short:36 – avg length (bp): – avg repeat %: 1.05%

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

VectorBase MMC1 runnable e! DB runnableDB runnable Exonerate BLAT ePCR DB record >> dna align object dna align object >> DB record MMC1_xrefreporter XREF

VectorBase MMC2 runnable e! DB runnableDB runnable Exonerate BLAT ePCR DB record >> marker object marker object >> DB record MMC2_xrefreporter XREF