1 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard Comparative Genome Annotation of Drosophila pseudoobscura and Its Implementation in chado

2 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard Drosophila phylogeny:

3 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard Annotation Methodology: Driven by orthology to Drosophila melanogaster (Dmel) genome (over annotated genes with protein isoforms) Focused on protein-coding genes TBLASTN: query: Dmel proteins subject: 8242 D. pseudoobscura (Dpse) WGS contigs Synteny, arm-ness conservation of fly genes obtained genomic locations of putative orthologs to Dmel genes.

4 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard Annotation Methodology (continued): Gene predictions: Genscan, Twinscan, Genewise (totally predictions) Gene predictions filtering: reciprocal best blastp hits (10515 predictions selected) Looking for overlap between predictions and TBLASTN ortholog calls, 9946 significantly overlapped predictions were promoted to be gene model annotations.

5 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard Annotation Methodology (continued): Mapping of Dpse genes FlyBase Curated from literature: ~500 FlyBase curated Dpse genes 134 one most representative GenBank accession 122unambiguous hits against Dpse WGS contigs 96merged with TBLASTN ortholog calls 18imported into Dpse annotation set as genetic loci on the genome.

6 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard Evidence data for Dpse annotation: BLASTZ HSPs between Dmel and Dpse: 34,576 Gene predictions Dpse EST alignments: 34,611 ESTs

7 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard Implementation of Comparative Data in Chado: Data objects: Orthologous Regions Genes Gene Models Syntenic Regions BLASTZ HSPs

8 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard Gene RNA Protein feature_relationship (subj->obj) Dpse Dmel putative_ortholog_of partof producedby Orthology Relationship

9 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard

10 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard

11 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard

12 GMOD Meeting, Spring 2005 Peili Zhang, FlyBase - Harvard Acknowledgement FlyBaseBaylor College of Medicine Bill GelbartStephen Richards Brian BettencourtYue Liu Pavel HradeckyKim Worley Stan LetovskyRui Chen David EmmertGeorge Weinstock Everyone at FlyBaseRichard Gibbs