1. Gene Prediction and Phylogenetic Trees
Jared Mimms

2. 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

3. Plant Genome Downloads

4. Other Downloadable Datasets

5. 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………..

6. 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

7. AGO4

8. Blasting Against Genome Database

9. Making Consensus

10. Concatenated Alignment

11. MUSCLE Alignment

12. Mr. Bayes Tree Builder
Wow 13:18:22

13. AGO4 Tree Posterior

14. AGO4 Tree

15. 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