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Vbi oomycetes2011 final
- 1. MycoCosm & JGI Oomycete Genomics Tools Andrea Aerts Eukaryotic Genomics Program US DOE Joint Genome Institute, Walnut Creek, CA <alaerts@lbl.gov>
- 3. 250+ people
- 5. Location: Walnut Creek, CAwww.jgi.doe.gov bioenergy, carbon cycling &biogeochemistry
- 6. 3 Are you in the right room? IMG MycoCosm 70+ annotated eukaryotic genomes genome.jgi-psf.org
- 8. MycoCosm
- 10. 6 Automated Annotation Pipeline Genome assembly and ESTs Repeat Masking Repeat Library Data Mapping External data sets Training predictors Gene Prediction Annotation External gene sets Quality Control Manual curation Optional Inputs Automated Pipeline Staged Portal Release
- 11. 7 Eukaryotic Gene Prediction Promoter TGA ATG PolyA GT AG Gene model 3’UTR 5’UTR exons introns mRNA Known genesare mapped onto genomic sequence Known gene Ab initiogene prediction is based on knowledge of general features of gene structure trained on a set of known genes. FGENESH GENEMARK Homology methods build exons around regions of homology and ensure gene structure features. Homolog Predicted model FGENESH+, GENEWISE
- 14. MycoCosm
- 16. 11 11 Genome-Centric View Focus:functional genomics, user data deposition and curation
- 17. 12 New Comparative View
- 18. 13 Community Building Tools Asilomar, Pacific Grove, CA (Mar 15-20): Mar 15: Dothideomycetes jamboree Mar 17: JGI Workshop (Fungi & CSP) Mar 18: Fungal Tools (MycoCosm) Walnut Creek, CA (Mar 21-24): Mar 21: Basidiomycetes jamboree Mar 22: MycoCosm tutorial 13
- 19. Oomycetes at JGI Phytophthoraramorum Phytophthorasojae improved assembly released “internally” in April 2011 Phytophthoracapsici Hybrid Sanger/454 assembly Public release November 2010 Phytophthoracinnamomi Currently in sequencing 14
- 21. MycoCosm
- 23. Manual Curation Workflow 17 Find a gene Validate gene structure Choose the best model Fix the structure or report the problems Annotate it!
- 26. Blat/Blast your sequence against genome, transcripts, proteins
- 28. 2. Validate Gene Structure, cont 20 Using Protein Pages, check: Alignments with homologs; Domains
- 29. 2. Validate Gene Structure, cont 21 Using Cluster Details pages, compare: sizes and domain composition of orthologs
- 32. Defline (mandatory, will go to GenBank)
- 34. Notes (‘No issues’ if the model is good)