FUNDING Grants from the NHGRI (P41HG002371 to G.B., H.C., M.D., P.F., A.H., F.H., D.K., V.K., W.J.K., R.K., C.L., L.M, B.R. and A.Z.; U41HG004568 to M.C., T.D., M.G., F.H., W.J.K., K.L., K.R. and B.R.); NCI (U24CA143858 to F.H. and W.J.K); subcontracts from the NIDCR (U01DE20057 to G.B. and R.K.), NHGRI (P01HG5062 to G.B., W.J.K. and B.R; U54HG004555 to M.D. and R.H.; U41HG004269 to A.H. and W.J.K.; U01HG004695 to W.J.K.); NICHD (RC2HD064525 to H.C., A.H. and R.K.); NIEHS (U01ES017154 to W.J.K). Support from HHMI to D.H. Funding for open access charges: HHMI. Conﬂict of interest statement. P.A.F., B.R., A.S.Z., A.S.H., D.K., G.P.B., H.C., M.D., T.R.D., B.M.G., R.A.H., F.H., V.K., R.M.K., K.L., C.H.L., L.R.M., A.P., B.J.R., K.R.R., K.E.S., D.H. and W.J.K. receive royalties from the sale of UCSC Genome Browser source code licenses to commercial entities. REFERENCES 1. Karolchik,D., Baertsch,R., Diekhans,M., Furey,T.S., Hinrichs,A., Lu,Y.T., Roskin,K.M., Schwartz,M., Sugnet,C.W., Thomas,D.J. et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res., 31, 51–54. 2. Rhead,B., Karolchik,D., Kuhn,R.M., Hinrichs,A.S., Zweig,A.S., Fujita,P.A., Diekhans,M., Smith,K.E., Rosenbloom,K.R., Raney,B.J. et al. (2010) The UCSC Genome Browser database: update 2010. Nucleic Acids Res., 38, D613–D619. 3. Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61–D65. 4. Pruitt,K.D., Tatusova,T., Klimke,W. and Maglott,D.R. (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res., 37, D32–D36. 5. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Sayers,E.W. (2010) GenBank. Nucleic Acids Res., 38, D46–D51. 6. Flicek,P., Aken,B.L., Ballester,B., Beal,K., Bragin,E., Brent,S., Chen,Y., Clapham,P., Coates,G., Fairley,S. et al. (2010) Ensembl’s 10th year. Nucleic Acids Res., 38, D557–D562. 7. Hsu,F., Kent,W.J., Clawson,H., Kuhn,R.M., Diekhans,M. and Haussler,D. (2006) The UCSC Known Genes. Bioinformatics, 22, 1036–1046. 8. Karolchik,D., Kuhn,R., Baertsch,R., Barber,G., Clawson,H., Diekhans,M., Giardine,B., Harte,R., Hinrichs,A., Hsu,F. et al. (2008) The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res., 36, D773–D779. 9. Blanchette,M., Kent,W.J., Riemer,C., Elnitski,L., Smit,A.F., Roskin,K.M., Baertsch,R., Rosenbloom,K., Clawson,H., Green,E.D. et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res., 14, 708–715. 10. Sayers,E.W., Barrett,T., Benson,D.A., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Edgar,R., Federhen,S. et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37, D5–D15. 11. The ENCODE Project Consortium. (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306, 636–640. 12. Thomas,D.J., Rosenbloom,K.R., Clawson,H., Hinrichs,A.S., Trumbower,H., Raney,B.J., Karolchik,D., Barber,G.P., Harte,R.A., Hillman-Jackson,J. et al. (2007) The ENCODE Project at UC Santa Cruz. Nucleic Acids Res., 35, D663–D667. 13. Rosenbloom,K.R., Dreszer,T.R., Pheasant,M., Barber,G.P., Meyer,L.R., Pohl,A., Raney,B.J., Wang,T., Hinrichs,A.S., Nucleic Acids Research, 2011, Vol. 39, Database issue D881 Zweig,A.S. et al. (2010) ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res., 38, D620–D625. 14. Karolchik,D., Hinrichs,A.S., Furey,T.S., Roskin,K.M., Sugnet,C.W., Haussler,D. and Kent,W.J. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res., 32, D493–D496. 15. Giardine,B., Riemer,C., Hardison,R.C., Burhans,R., Elnitski,L., Shah,P., Zhang,Y., Blankenberg,D., Albert,I., Taylor,J. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451–1455. 16. Kent,W.J. (2002) BLAT–the BLAST-like alignment tool. Genome Res., 12, 656–664. 17. Kent,W.J., Hsu,F., Karolchik,D., Kuhn,R.M., Clawson,H., Trumbower,H. and Haussler,D. (2005) Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res., 15, 737–741. 18. Hsu,F., Pringle,T.H., Kuhn,R.M., Karolchik,D., Diekhans,M., Haussler,D. and Kent,W.J. (2005) The UCSC Proteome Browser. Nucleic Acids Res., 33, D454–D458. 19. Kuhn,R.M., Karolchik,D., Zweig,A.S., Trumbower,H., Thomas,D.J., Thakkapallayil,A., Sugnet,C.W., Stanke,M., Smith,K.E., Siepel,A. et al. (2007) The UCSC Genome Browser Database: update 2007. Nucleic Acids Res., 35, D668–D673. 20. Kent,W.J., Zweig,A.S., Barber,G., Hinrichs,A.S. and Karolchik,D. (2010) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics, 26, 2204–2207. 21. Li,H., Handsaker,B., Wysoker,A., Fennell,T., Ruan,J., Homer,N., Marth,G., Abecasis,G. and Durbin,R. and 1000_Genome_Project_ Data_Processing_Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078–2079. 22. McLean,C.Y., Bristor,D., Hiller,M., Clarke,S.L., Schaar,B.T., Lowe,C.B., Wenger,A.M. and Bejerano,G. (2010) GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol., 28, 495–501. 23. Green,R.E., Krause,J., Briggs,A.W., Maricic,T., Stenzel,U., Kircher,M., Patterson,N., Li,H., Zhai,W., Fritz,M.H. et al. (2010) A draft sequence of the Neandertal genome. Science, 328, 710–722. 24. Green,R.E., Malaspinas,A.S., Krause,J., Briggs,A.W., Johnson,P.L., Uhler,C., Meyer,M., Good,J.M., Maricic,T., Stenzel,U. et al. (2008) A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell, 134, 416–426. 25. Firth,H.V., Richards,S.M., Bevan,A.P., Clayton,S., Corpas,M., Rajan,D., Van Vooren,S., Moreau,Y., Pettett,R.M. and Carter,N.P. (2009) DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am. J. Hum. Genet., 84, 524–533. 26. Hindorff,L.A., Sethupathy,P., Junkins,H.A., Ramos,E.M., Mehta,J.P., Collins,F.S. and Manolio,T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362–9367. 27. Kiran,A. and Baranov,P.V. (2010) DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics, 26, 1772–1776. 28. Romanov,M.N., Tuttle,E.M., Houck,M.L., Modi,W.S., Chemnick,L.G., Korody,M.L., Mork,E.M., Otten,C.A., Renner,T., Jones,K.C. et al. (2009) The value of avian genomics to the conservation of wildlife. BMC Genomics, 10(Suppl. 2), S10. 29. Iafrate,A.J., Feuk,L., Rivera,M.N., Listewnik,M.L., Donahoe,P.K., Qi,Y., Scherer,S.W. and Lee,C. (2004) Detection of large-scale variation in the human genome. Nat. Genet., 36, 949–951. 30. Feuk,L., Carson,A.R. and Scherer,S.W. (2006) Structural variation in the human genome. Nat. Rev. Genet., 7, 85–97. 31. Lamesch,P., Li,N., Milstein,S., Fan,C., Hao,T., Szabo,G., Hu,Z., Venkatesan,K., Bethel,G., Martin,P. et al. (2007) hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics, 89, 307–315. 32. Ahn,S.M., Kim,T.H., Lee,S., Kim,D., Ghang,H., Kim,D.S., Kim,B.C., Kim,S.Y., Kim,W.Y., Kim,C. et al. (2009) The ﬁrst Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res., 19, 1622–1629. 33. Sherry,S., Ward,M.-H., Kholodov,M., Baker,J., Phan,L., Smigielski,E. and Sirotkin,K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308–311.