gene prediction and phylogenetic trees jared mimms
TRANSCRIPT
Gene Prediction and Phylogenetic Trees
Jared Mimms
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
Plant Genome Downloads
http://phytozome.net
Other Downloadable Datasets
http://www.plantgdb.org
https://strawberry.plantandfood.co.nz/gbrowse/navbar/strawberry/download.html
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………..
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
AGO4
Blasting Against Genome Database
Making Consensus
Concatenated Alignment
MUSCLE Alignment
Mr. Bayes Tree Builder
Wow13:18:22
AGO4 Tree Posterior
AGO4 Tree
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