Gene Prediction and Phylogenetic Trees Jared Mimms.
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Transcript of Gene Prediction and Phylogenetic Trees Jared Mimms.
![Page 1: Gene Prediction and Phylogenetic Trees Jared Mimms.](https://reader030.fdocuments.net/reader030/viewer/2022033022/56649efd5503460f94c1131a/html5/thumbnails/1.jpg)
Gene Prediction and Phylogenetic Trees
Jared Mimms
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Using Geneious and Internal Blast
• Genbank deficient• Make databases – Illumina Contigs– 454 Scaffolds– ESTs– Other plant genomes
• Search for genes using internal BLAST• Create consensus sequence combining all
BLAST matches on a particular contig/scaffold
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Plant Genome Downloads
http://phytozome.net
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Other Downloadable Datasets
http://www.plantgdb.org
https://strawberry.plantandfood.co.nz/gbrowse/navbar/strawberry/download.html
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My Databases• Citris clementina• Citris sinensis• Manihot esculenta• Mimulus guttatus• Ricinus communis• Oryza sativa• Carica papaya• Fragaria vesca• Zea mays• Vitis choloroplast• Arabidopsis chloroplast
• And Growing………..
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Example: AGO4
• BLASTn Arabidopsis vs. Genome Databases• Select all hits from same
contig/scaffold/BAC/chromosome• Concatenate hits relative to Arabidopsis AGO4
gene (coding and noncoding segments)• Isolate predicted gene• Repeat for many species• Run MUSCLE alignment• Run MrBayes phylogenetic analysis
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AGO4
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Blasting Against Genome Database
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Making Consensus
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Concatenated Alignment
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MUSCLE Alignment
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Mr. Bayes Tree Builder
Wow13:18:22
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AGO4 Tree Posterior
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AGO4 Tree
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Future Directions
• It’s go time baby…• ramp up to methytransferases • Standardize annotation formats (.xml)• CG analysis, role in CpG, CpNpG methylation• Promoter anlayses• Trees for entire genome• Get scaffolders up and running (Bambus)
(need paired end?)Expand database to all publically available organism sequencing
data (download all ftp’s)Internal Cloud