Information de reference pour ce titreAccession Number: | 00006178-200937001-00135.
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Author: | Kuhn, R. M. 1,*; Karolchik, D. 1; Zweig, A. S. 1; Wang, T. 1; Smith, K. E. 1; Rosenbloom, K. R. 1; Rhead, B. 1; Raney, B. J. 1; Pohl, A. 1; Pheasant, M. 1; Meyer, L. 1; Hsu, F. 1; Hinrichs, A. S. 1; Harte, R. A. 1; Giardine, B. 2; Fujita, P. 1; Diekhans, M. 1; Dreszer, T. 1; Clawson, H. 1; Barber, G. P. 1; Haussler, D. 1,3; Kent, W. J. 1
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Institution: | (1)Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA (2)Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA (3)Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
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Title: | The UCSC Genome Browser Database: update 2009.[Article]
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Source: | Nucleic Acids Research. 37 (Database issue):D755-D761, January 2009.
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Abstract: | The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu- ouverture dans une nouvelle fenêtre) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.
(C) Copyright Oxford University Press 2009.
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References: | 1. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, et al. The UCSC genome browser database. Nucleic Acids Res. (2003) 31:51-54.
2. Hinrichs A, Karolchik D, Baertsch R, Barber G, Bejerano G, Clawson H, Diekhans M, Furey T, Harte R, Hsu F, et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. (2006) 34:D590-D598.
3. Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, et al. The UCSC Genome Browser Database: update 2007. Nucleic Acids Res. (2007) 35:D668-D673.
4. Karolchik D, Kuhn R, Baertsch R, Barber G, Clawson H, Diekhans M, Giardine B, Harte R, Hinrichs A, Hsu F, et al. The UCSC genome browser database: 2008 update. Nucleic Acids Res. (2008) 36:D773-D779.
5. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, et al. Ensembl 2008. Nucleic Acids Res. (2008) 36:D707-D714.
6. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. (2008) 36:D13-D21.
7. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res. (2008) 36:D25-D30.
8. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. (2007) 35:D61-D65.
9. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. (2004) 14:708-715.
10. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, et al. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. (2004) 14:2121-2127.
11. Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S, et al. The international gene trap consortium website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. (2006) 34:D642-D648.
12. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. Detection of large-scale variation in the human genome. Nat. Genet. (2004) 36:949-951.
13. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC table browser data retrieval tool. Nucleic Acids Res. (2004) 32:D493-D496.
14. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Miller W, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. (2005) 15:1451-1455.
15. Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. (2005) 15:737-741.
16. Hsu F, Pringle TH, Kuhn RM, Karolchik D, Diekhans M, Haussler D, Kent WJ. The UCSC proteome browser. Nucleic Acids Res. (2005) 33:D454-D458.
17. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res. (2002) 12:656-664.
18. Encode Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science (2004) 306:636-640.
19. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl Acad. Sci. USA (2003) 100:11484-11489.
20. Kosiol C, Vinar T, da Fonseca R, Hubisz M, Bustamante C, Nielsen R, Siepel A. Patterns of positive selection in six mammalian genomes. PLoS Genet. (2008) 4:e1000144.
21. Yang Z, Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. (2002) 19:908-917.
22. Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. (2008) 36:D107-D113.
23. Kidd J, Cooper G, Donahue W, Hayden H, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, et al. Mapping and sequencing of structural variation from eight human genomes. Nature (2008) 453:56-64.
24. The International HapMap Consortium. The international hapmap project. Nature (2003) 426:789-796.
25. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou MM, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. (2005) 15:1034-1050.
26. Griffiths-Jones S, Saini HK, Dongen SV, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. (2008) 36:D154-D158.
27. Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ, RGD_Team. The Rat Genome Database, update 2007-easing the path from disease to data and back again. Nucleic Acids Res. (2007) 35:D658-D662.
28. Bellen HJ, Levis RW, Liao G, He Y, Carlson JW, Tsang G, Evans-Holm M, Hiesinger PR, Schulze KL, Rubin GM, et al. The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes. Genetics (2004) 167:761-781.
29. The UniProt Consortium. The universal protein resource (UniProt). Nucleic Acids Res. (2008) 36:D190-D195.
30. Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA, The Mouse Genome Database Group. The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res. (2008) 36:D724-D728.
31. Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, et al. The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res. (2008) 36:D768-D772.
32. Rogers A, Antoshechkin I, Bieri T, Blasiar D, Bastiani C, Canaran P, Chan J, Chen WJ, Davis P, Fernandes J, et al. Wormbase 2007. Nucleic Acids Res. (2008) 36:D612-D617.
33. Wilson RJ, Goodman JL, Strelets VB, The FlyBase Consortium. FlyBase: integration and improvements to query tools. Nucleic Acids Res. (2008) 36:D588-D593.
34. Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, et al. Gene ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. (2008) 36:D577-D581.
35. Bruford EA, Lush MJ, Wright MW, Sneddon TP, Povey S, Birney E. The HGNC database in 2008: a resource for the human genome. Nucleic Acids Res. (2008) 36:D445-D448.
36. Yu W, Gwinn M, Clyne M, Yesupriya A, Khoury MJ. A navigator for human genome epidemiology. Nat. Genet. (2008) 40:124-125.
37. Mattes WB, Pettit SD, Sansone S.-A, Bushel PR, Waters MD. Database development in toxicogenomics: issues and efforts. Environ. Health Perspect. (2004) 112:495-505.
38. Sherry S, Ward M-H, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. (2001) 29:308-311.
39. Zhu J, Sanborn J, Diekhans M, Lowe C, Pringle T, Haussler D. Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput. Biol. (2007) 3:e247.
40. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. (2003) 13:103-107.
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Language: | English.
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Document Type: | ARTICLE.
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Journal Subset: | Life & Biomedical Sciences.
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ISSN: | 0305-1048
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NLM Journal Code: | o8l, 0411011
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