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UCSC Genome Browser

UCSC Genome Browser. Robert Kuhn, PhD Center for Biomolecular Science and Engineering University of California, Santa Cruz FaceBase kick-off meeting Bethesda, MD November 16, 2009. Thanks!. Funding: NHGRI, NCI, NICHD, NIDCR, HHMI, QB3, SU2C

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UCSC Genome Browser

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  1. UCSC Genome Browser Robert Kuhn, PhDCenter for Biomolecular Science and EngineeringUniversity of California, Santa Cruz FaceBase kick-off meeting Bethesda, MD November 16, 2009

  2. Thanks! • Funding: NHGRI, NCI, NICHD, NIDCR, HHMI, QB3, SU2C • Data: NCBI, Ensembl, UniProt, 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 – KiloKluster, Sys-admin

  3. Browser: interface to database browser primary table  track (mapping)  details secondary tables software tables database

  4. Genome Browser traffic > 3 million hits / wk 80,000 distinct IPs / mo

  5. Genome Browser 44-species conservation ucsc browsers on high-coverage assemblies FaceBase mirror

  6. FOXE1 gene chromBand OMIM UCSC Genes SNPs Conservation

  7. Genome Browser saving/sharing sessions save a session

  8. Variation Resources • chromosome 2q21.2 – 2q21.3 HapMap phased LD

  9. Custom Tracks • View private data in context of all other UCSC-hosted data. • Intersect with public data. • Save custom track data in Sessions.

  10. Custom Tracks • Show gain and loss of copies on chrom arm 2q gain loss

  11. Genome Graphs • Export Custom Track data to Genome Graphs

  12. Genome Graphs for association studies

  13. Visigene

  14. Visigene zoom in on in-situs

  15. UCSC Browser Mirrors mirror sites: Duke Cornell Medical College of Wisconsin Copenhagen Brisbane see also wikipedia for links

  16. UCSC Browser Help mailing list + archives

  17. UCSC Browser Training Online / Onsite training UCSC Open Helix

  18. Variation Resources • chromosome Xq26.3 dbSNP 129 Database of Genomic Variants Segmental Duplications

  19. Sessions / Custom wiggle*just for funuser: Hiramsession: moneyPolitics

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