The UCSC genome browser and associated tools

Briefings in Bioinformatics

Volumn 14, Issue 2, 2013, Pages 144-161

  Kuhn, Robert M ^a   Haussler, David ^a,b   James Kent, W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Bioinformatics; Genetics; Genomics; Human genome; Sequencing; UCSC genome browser

Indexed keywords

ANIMAL; ARTICLE; BIOLOGY; COMPUTER GRAPHICS; COMPUTER PROGRAM; DATA MINING; GENETIC DATABASE; GENOMICS; HUMAN; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERNET; SEARCH ENGINE; SEQUENCE ALIGNMENT; STATISTICS;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DATA DISPLAY; DATA MINING; DATABASES, GENETIC; GENOMICS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; SEARCH ENGINE; SEQUENCE ALIGNMENT; SOFTWARE;

VERTEBRATA;

EID: 84875608234     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbs038     Document Type: Article

References (49)

1. Kent WJ, Sugnet CW, Furey TS, et al. The Human Genome Browser at UCSC. Genome Res 2002;12:996-1006.
2. Fujita PA, Rhead B, Zweig AS, et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res 2011;39: D876-82.
3. Dreszer TR, Karolchik D, Zweig AS, et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res 2012;40:D918-23.
4. Kuhn RM, Karolchik D, Zweig AS, et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 2009;37:D755-61.
5. Rhead B, Karolchik D, Kuhn RM, et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res 2010;38:D613-9.
6. Flicek P, Amode MR, Barrell D, et al. Ensembl 2012. Nucleic Acids Res 2012;40:D84-90.
7. Stein LD, Mungall C, Shu S, et al. The generic genome browser: a building block for a model organism system database. Genome Res 2002;12:1599-610.
8. Robinson JT, Thorvaldsdóttir H, Winckler W, et al. Integrative genomics viewer. Nature Biotechnology 2011;29: 24-6.
9. Kent WJ, Haussler D. Assembly of the working draft of the human genome with GigAssembler. Genome Res 2001;11: 1541-8.
10. The International Human Genome Mapping Consortium. A physical map of the human genome. Nature 2001;409: 934-41.
11. Pruitt KD, Katz KS, Sicotte H, et al. Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet 2000;16:44-7.
12. Flicek P, Aken BL, Ballester B, et al. Ensembl's 10th year. Nucleic Acids Res 2010;38:D557-62.
13. Kent WJ, Zahler AM. The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans. Nucleic Acids Res 2000;28:91-3.
14. Jurka J, Kapitonov VV, Pavlicek A, et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res 2005;110:462-7.
15. Benson DA, Karsch-Mizrachi I, Lipman DJ, et al. GenBank. Nucleic Acids Res 2011;39:D32-7.
16. Gross S, Brent MR. Using multiple alignments to improve gene prediction. JComputBiol 2006;13:379-93.
17. Flicek P, Amode MR, Barrell D, et al. Ensembl 2011. Nucleic Acids Res 2011;39:D800-6.
18. Hsu F, Kent WJ, Clawson H, et al. The UCSC Known Genes. Bioinformatics 2006;22:1036-46.
19. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002;12:656-64.
20. Kent WJ, Baertsch R, Hinrichs A, et al. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. ProcNatlAcad SciUSA 2003;100:11484-9.
21. Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-402.
22. Blanchette M, Kent WJ, Riemer C, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004;14:708-15.
23. Siepel A, Bejerano G, Pedersen JS, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005;15:1034-50.
24. Siepel A, Pollard KS, Haussler D. New methods for detecting lineage-specific selection. Proceedings of the 10th International Conference on Research in Computational Molecular Biology (RECOMB 2006) 2006;3909:190-205.
25. Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nature Genetics 2004;36: 949-51.
26. Firth HV, Richards SM, Bevan AP, et al. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. AmJHum Genet 2009; 84:524-33.
27. Su AI, Wiltshire T, Batalov S, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad SciUSA 2004;101:6062-7.
28. Bailey JA, Gu Z, Clark RA, et al. Recent segmental duplications in the human genome. Science 2002;297:1003-7.
29. Raney BJ, Cline MS, Rosenbloom KR, et al. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res 2011;39:D871-5.
30. Sherry S, Ward M-H, Kholodov M, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001; 29:308-311.
31. Amberger J, Bocchini CA, Scott AF, et al. McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res 2009;37:D793-6.
32. Bernstein BE, Stamatoyannopoulos JA, Costello JF, et al. The NIH Roadmap Epigenomics Mapping Consortium. Nature Biotechnology 2010;28:1045-8.
33. ENCODE Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004;306:636-40.
34. The ENCODE Project Consortium, Birney E, Stamatoyannopoulos J, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007;447:799-816.
35. Safran M, Chalifa-Caspi V, Shmueli O, et al. Human gene-centric databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. Nucleic Acids Res 2003;31:142-6.
36. Pagon RA, Tarczy-Hornoch P, Baskin PK, et al. GeneTests-GeneClinics: genetic testing information for a growing audience. HumanMutation 2002;19:501-9.
37. Bruford EA, Lush MJ, Wright MW, et al. The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res 2008;36:D445-8.
38. Bult CJ, Eppig JT, Kadin JA, et al. The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res 2008;36:D724-8.
39. The UniProt Consortium. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 2010;38:D142-8.
40. Ruan J, Li H, Chen Z, et al. TreeFam: 2008 Update. Nucleic Acids Res 2008;36:D735-40.
41. Kent WJ, Zweig AS, Barber G, et al. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 2010;26:2204-7.
42. Li H, Handsaker B, Wysoker A, et al. The Sequence alignment/ map (SAM) format and SAMtools. Bioinformatics 2009;25:2078-9.
43. Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools. Bioinformatics 2011;27:2156-8.
44. Kaiser J. A plan to capture human diversity in 1000 genomes. Science 2008;319:395.
45. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nature Rev Genet 2006;7:85-97.
46. Church DM, Lappalainen I, Sneddon TP, et al. Public data archives for genomic structural variation. Nature Genetics 2010;42:813-4.
47. Cooper GM, Coe BP, Girirajan S, et al. A copy number variation morbidity map of developmental delay. Nature Genetics 2011;43:838-46.
48. McLaren W, Pritchard B, Rios D, et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 2010;26:2069-70.
49. Genome 10K Community of Scientists. Genome 10 K: A Proposal to Obtain Whole-Genome Sequence for 10,000 Vertebrate Species. JHered 2009;100:659-74.