Vectorbase probe mapping

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Vectorbase probe mapping
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vectorbase
Manual Annotation
CHADO
XML
browser
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Integration aims

• Contigview
• View alignment track
• Geneview
• Reporters
• experiments
• Expression patterns?

• Reporter page
• Positions mapped
• Genes overlapped
• Experiments used in

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contigview
Linked to location Feature track Link to
BASE Detail popup st-end, name, id
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geneview
Associated with gene Reporter Experiments(?)
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DAS Vs. e!

• Slow
• Delayed data flow
• Limited scope for adaptation
• a load of links

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DAS - requestresponse
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data flow
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2
3
name chrstart-endstrand
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DAS Vs. e!

• 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

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affy feature
cf affy_feature
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featureview
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e! features
est sequences
gt 97 identity gt 90 coverage
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probe types

• MMC1
• Spotted array cDNA clones
• MMC2
• Spotted array PCR products
• Affy
• Short oligo tiling path
• Agilent
• Long oligo, tiling path?

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1 - est2reporter
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2 - est2reporter
est1
300bp
est2
500bp
3R
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3 - est2reporter
est1
50bp
est2
500bp
est1
2L
est2
est2
est2
3R
est2
est2
est2
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pcr2reporter
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sts pipeline
id left_primer right_primer distance name accession species
1.1.1 GATTACAACATCCAGAAGGAGTC GTAGTACTTGAGGACAGCAAG 104 ENSANGG00000020724 ENSANGG00000020724 A.gambiae
1.1.10 GCCTTTGCCGGGCTGC TTCGGGGGTTTCGAGCAG 497 ENSANGG00000002666 ENSANGG00000002666 A.gambiae
1.1.11 GATAATTCAGCGCTACACATTA CACCGTAATGCTAACATCGAA 146 ENSANGG00000002705 ENSANGG00000002705 A.gambiae
1.1.11 GATAATTCAGCGCTACACATTA CACCGTAATGCTAACATCGAA 146 ENSANGG00000020019 ENSANGG00000020019 A.gambiae
1.1.12 CAGTGCTACGTGAAGAATGA TCCGCTGTCGAGGGAAC 473 ENSANGG00000003095 ENSANGG00000003095 A.gambiae
1.1.2 TCGTCCAACAGTTTCTCCTAC GATCGTTTGCTGCTTGCATA 449 ENSANGG00000000521 ENSANGG00000000521 A.gambiae
2L
3R
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1 - reporter2gene
2L
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2 - reporter2gene
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MMC1 locations
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MMC1 locations table
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MMC1 genes
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MMC1 genes table
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MMC2 locations
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MMC2 genes
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MMC2 table
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MMC DAS tracks
http//base.vectorbase.org8080/das
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MMC listings
http//base.vectorbase.org8080/MMC1.jsp http//ba
se.vectorbase.org8080/MMC2.jsp
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fin

• Thanks
• Bob, George, Fotis
• Dan, Karyn, Martin _at_ EBI
• Ian Sealy _at_ Sanger
• Informatics support _at_ Sanger

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EST quality

• TOTAL 19280
• OK 17186 (89.14)
• POOR 2094 (10.86)
• repetitive 2094
• short 36
• avg length (bp) 576.39
• avg repeat 1.05

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general runnable
Exonerate
DB record gtgt perl object
e! DB
runnable
runnableDB
BLAT
get object from db
ePCR
perl object gtgt DB record
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MMC1 runnable
Exonerate
DB record gtgt dna align object
e! DB
runnable
runnableDB
BLAT
MMC1_xref
reporter XREF
ePCR
dna align object gtgt DB record
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MMC2 runnable
Exonerate
DB record gtgt marker object
e! DB
runnable
runnableDB
BLAT
MMC2_xref
reporter XREF
ePCR
marker object gtgt DB record