anper - anthocyanin permease aomt - anthocyanin o-methyltransferase chi - chalcone isomerase dfr -...
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ANPER - anthocyanin permeaseAOMT - anthocyanin O-methyltransferaseCHI - chalcone isomeraseDFR - dihydroflavonol 4-reductaseF3’H - flavonoid 3' hydroxylaseLDOX - leucoanthocyanidin dioxygenaseFLS- flavonol synthaseMyba1 - myb-related transcription factorMycA1 - myc anthocyanin regulatory proteinUFGT - UDP-glucose:flavonoid 3-O-glucosyltransferase
Allan Brown’s Wish List: EST Results
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ANPER - anthocyanin permease
Allan Brown’s Wish List: EST Results
Towson Database
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ANPER - anthocyanin permease
gb|AY348872.1| Lycopersicon esculentum putative anthocyanin permease mRNA, complete cds
BLAST match
Allan Brown’s Wish List: EST Results
Towson DatabaseBLAST verifiedBLAST invalid ESTBLAST surprise, wrong but interesting
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ANPER - anthocyanin permease
http://www.ncbi.nlm.nih.gov/nucest/DR067294
Allan Brown’s Wish List: EST Results
WSU Database
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ANPER - anthocyanin permease
http://www.ncbi.nlm.nih.gov/nucest/DR067294
PREDICTED: Vitis vinifera protein TRANSPARENT TESTA 12-like (LOC100250967),
BLAST match
Allan Brown’s Wish List: EST Results
WSU DatabaseBLAST verifiedBLAST invalid ESTBLAST surprise, wrong but interesting
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AOMT - anthocyanin O-methyltransferase
http://www.ncbi.nlm.nih.gov/nucest/DW043195
Allan Brown’s Wish List: EST Results
WSU Database
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AOMT - anthocyanin O-methyltransferase
http://www.ncbi.nlm.nih.gov/nucest/DW043195
Rhododendron catawbiense early light-induced protein 7 mRNA,BLAST match
Allan Brown’s Wish List: EST Results
WSU Database
BLAST verifiedBLAST invalid ESTBLAST surprise, wrong but interesting
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CHI - chalcone isomerasehttp://www.ncbi.nlm.nih.gov/nucest/CF810723
http://www.ncbi.nlm.nih.gov/nucest/CV190427
Allan Brown’s Wish List: EST Results
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CHI - chalcone isomerasehttp://www.ncbi.nlm.nih.gov/nucest/CF810723
http://www.ncbi.nlm.nih.gov/nucest/CV190427
component of oligomeric golgi complex 6BLAST match
BLAST matchLiriodendron tulipifera clone BAC125P15 FLORICAULA/LEAFY-like protein, glycyl-tRNA synthetase-like protein, and VARIANT IN METHYLATION-like protein genes, complete cds; and integral membrane protein gene, partial cds
Allan Brown’s Wish List: EST ResultsBLAST verifiedBLAST invalid ESTBLAST surprise, wrong but interesting
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DFR - dihydroflavonol 4-reductase
http://www.ncbi.nlm.nih.gov/nucest/DW043076
http://www.ncbi.nlm.nih.gov/nucest/CV091566
Allan Brown’s Wish List: EST Results
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DFR - dihydroflavonol 4-reductase
http://www.ncbi.nlm.nih.gov/nucest/DW043076
http://www.ncbi.nlm.nih.gov/nucest/CV091566
BLAST match
BLAST match
Vaccinium macrocarpon dihydroflavonol 4-reductase mRNA
Vitis vinifera dihydroflavonol-4-reductase-like (LOC100267635)
Allan Brown’s Wish List: EST Results
BLAST verifiedBLAST invalid ESTBLAST surprise, wrong but interesting
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F3’H - flavonoid 3' hydroxylase
Allan Brown’s Wish List: EST Results
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LDOX - leucoanthocyanidin dioxygenase
http://www.ncbi.nlm.nih.gov/nucest/CV091044
http://www.ncbi.nlm.nih.gov/nucest/CV190548
http://www.ncbi.nlm.nih.gov/nucest/CV191078
Allan Brown’s Wish List: EST Results
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LDOX - leucoanthocyanidin dioxygenase
http://www.ncbi.nlm.nih.gov/nucest/CV091044
http://www.ncbi.nlm.nih.gov/nucest/CV190548
http://www.ncbi.nlm.nih.gov/nucest/CV191078
BLAST match
BLAST match
Vaccinium corymbosum anthocyanidin synthase (ans) mRNA
Vaccinium corymbosum anthocyanidin synthase (ans) mRNA
Allan Brown’s Wish List: EST Results
BLAST verifiedBLAST invalid ESTBLAST surprise, wrong but interesting
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FLS- flavonol synthase
http://www.ncbi.nlm.nih.gov/nucest/CV091044
Allan Brown’s Wish List: EST Results
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FLS- flavonol synthase
http://www.ncbi.nlm.nih.gov/nucest/CV091044
BLAST match
Antirrhinum hispanicum slf-S5 gene for S locus F-box (SLF)-S5 protein and slf-S5A gene for S locus F-box (SLF)-S5A protein
Allan Brown’s Wish List: EST Results
BLAST verifiedBLAST invalid ESTBLAST surprise, wrong but interesting
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Myba1 - myb-related transcription factor
http://www.ncbi.nlm.nih.gov/nucest/DR067494
http://www.ncbi.nlm.nih.gov/nucest/CV091396
http://www.ncbi.nlm.nih.gov/nucest/CV191530
http://www.ncbi.nlm.nih.gov/nucest/CV090776
Allan Brown’s Wish List: EST Results
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Myba1 - myb-related transcription factor
http://www.ncbi.nlm.nih.gov/nucest/DR067494
http://www.ncbi.nlm.nih.gov/nucest/CV091396
http://www.ncbi.nlm.nih.gov/nucest/CV191530
http://www.ncbi.nlm.nih.gov/nucest/CV090776
Rubus idaeus Myb-related transcription factor gene
Populus trichocarpa predicted protein (MYB084)
Vaccinium myrtillus MYB1-like mRNA
Malus x domestica MYB24 mRNA, complete cds
Allan Brown’s Wish List: EST ResultsBLAST verifiedBLAST invalid EST
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MycA1 - myc anthocyanin regulatory protein
Allan Brown’s Wish List: EST Results
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UFGT - UDP-glucose:flavonoid 3-O-glucosyltransferase
http://www.ncbi.nlm.nih.gov/nucest/CV091309
http://www.ncbi.nlm.nih.gov/nucest/DR067838
Allan Brown’s Wish List: EST Results
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UFGT - UDP-glucose:flavonoid 3-O-glucosyltransferase
http://www.ncbi.nlm.nih.gov/nucest/CV091309
http://www.ncbi.nlm.nih.gov/nucest/DR067838
BLAST match
BLAST match
Actinidia chinensis flavonoid 3-0-galactosyltransferase mRNA
Actinidia chinensis flavonoid 3-0-galactosyltransferase mRNA
Allan Brown’s Wish List: EST ResultsBLAST verifiedBLAST invalid EST
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ANPER - anthocyanin permeaseAOMT - anthocyanin O-methyltransferaseCHI - chalcone isomeraseDFR - dihydroflavonol 4-reductaseF3’H - flavonoid 3' hydroxylaseLDOX - leucoanthocyanidin dioxygenaseFLS- flavonol synthaseMyba1 - myb-related transcription factorMycA1 - myc anthocyanin regulatory proteinUFGT - UDP-glucose:flavonoid 3-O-glucosyltransferase
BLAST verifiedBLAST invalid ESTBLAST surprise, wrong but interesting
Allan Brown’s Wish List: EST Results
![Page 23: ANPER - anthocyanin permease AOMT - anthocyanin O-methyltransferase CHI - chalcone isomerase DFR - dihydroflavonol 4-reductase F3H - flavonoid 3' hydroxylase](https://reader035.vdocuments.mx/reader035/viewer/2022062619/5518d20055034638098b5101/html5/thumbnails/23.jpg)
ANPER – short, 3’ end of scaffoldAOMT – tBLASTn carboxyl end protein, 3’ end scaffoldCHI – big chunk of scaffold near SSR siteDFR – grape cDNAF3’H - big chunk of scaffold near SSR siteLDOX – medium chunk from scaffoldFLS - big chunk of scaffoldMyba1 – tBLASTn with peptide sequenceMycA1 - big chunk of scaffoldUFGT - tBLASTn with peptide sequence
Best Methods – avoid big scaffold chunksBLAST verifiedBLAST invalid ESTBLAST surprise, wrong but interesting
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1) BLAST grape (other plant) cDNA or protein sequence
2) collect scaffold hits (threshold E value < 0.001)
3) automatically BLAST scaffold against ESTs
4) Return full EST sequences and sources
5) From results:
• Allow all ESTs to be BLASTed against NCBI to ID
• All ESTs to be BLASTed against blueberry genome
What tool do we need to improve system?
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1) Query ESTs and genome annotations with EC numbers
2) Web site that ranks SSR results: (user inputs)
3) Align ESTs or cDNAs with scaffolds to find introns
4) Tool for collecting all allele or paralog scaffolds
5) Visualize aligned sequences from #4
6) Visualize KEGG pathway map with personal results
7) Compare blueberry and grape annotations
What tool do we need to improve system?