UCSC Genome Browser Robert Kuhn Ph D Center
UCSC Genome Browser Robert Kuhn, Ph. D Center for Biomolecular Science and Engineering University of California, Santa Cruz Face. Base kick-off meeting Bethesda, MD November 16, 2009
Thanks! • Funding: NHGRI, NCI, NICHD, NIDCR, HHMI, QB 3, SU 2 C • Data: NCBI, Ensembl, Uni. Prot, Baylor, WUSTL, UWash, IMIM, OMIM, numerous other contributors • UCSC Browser team: – David Haussler – PI – Jim Kent – Browser Concept, BLAT, Team Leader, Co-PI – Mark Diekhans, Fan Hsu, Angie Hinrichs, Kate Rosenbloom, Hiram Clawson, Rachel Harte, Galt Barber, Andy Pohl, Tim Dreszer, Larry Meyer, Mike Pheasant, Brian Raney, Melissa Cline – Engineering – Donna Karolchik, Robert Kuhn, Ann Zweig, Kayla Smith, Brooke Rhead, Pauline Fujita, Katrina Learned – QA, Docs, Support – Ting Wang, Jing Zhu, Steve Benz, Zach Sanborn – Cancer Browser – Jorge Garcia, Victoria Lin, Erich Weiler, Alex Wolfe – Kilo. Kluster, Sysadmin
Browser: interface to database browser software primary tables track (mapping) details secondary tables database
Genome Browser traffic > 3 million hits / wk 80, 000 distinct IPs / mo
Genome Browser 44 -species conservation ucsc browsers on high-coverage assemblies Face. Base mirror
FOXE 1 gene chrom. Band OMIM UCSC Genes SNPs Conservation
Genome Browser saving/sharing sessions save a session
Variation Resources • chromosome 2 q 21. 2 – 2 q 21. 3 Hap. Map phased LD
Custom Tracks • View private data in context of all other UCSC-hosted data. • Intersect with public data. • Save custom track data in Sessions.
Custom Tracks • Show gain and loss of copies on chrom arm 2 q gain loss
Genome Graphs • Export Custom Track data to Genome Graphs
Genome Graphs for association studies
Visigene
Visigene zoom in on in-situs
UCSC Browser Mirrors mirror sites: Duke Cornell Medical College of Wisconsin Copenhagen Brisbane see also wikipedia for links
UCSC Browser Help mailing list + archives
UCSC Browser Training Online / Onsite training UCSC Open Helix
Variation Resources • chromosome Xq 26. 3 db. SNP 129 Database of Genomic Variants Segmental Duplications
Sessions / Custom wiggle *just for fun user: Hiram session: money. Politics
- Slides: 26