SeqWare Query Engine: Storing and searching sequence data in the cloud

BMC Bioinformatics

Volumn 11, Issue SUPPL. 12, 2010, Pages

  O'Connor, Brian D ^a   Merriman, Barry ^b   Nelson, Stanley F ^b  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL RESEARCH; CLINICAL APPLICATION; CLOUD COMPUTING TECHNOLOGIES; COMPUTATIONAL INFRASTRUCTURE; GLIOBLASTOMA MULTIFORME; INTERACTIVE QUERIES; NEXT-GENERATION DNA SEQUENCERS; TUNING OF PARAMETERS;

CELL CULTURE; CLOUD COMPUTING; COMPUTER PROGRAMMING; ENGINES; GENES; OPEN SYSTEMS; QUERY PROCESSING; TOOLS;

SEARCH ENGINES;

ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; METHODOLOGY; NUCLEIC ACID DATABASE;

DATABASES, NUCLEIC ACID; GENOME, HUMAN; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 78650802666     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S12-S2     Document Type: Article

References (30)

1. Snyder M, Du J, Gerstein M. Personal genome sequencing: current approaches and challenges. Genes & development 2010, 24(5):423. 10.1101/gad.1864110, 2827837, 20194435.
2. Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860-921. 10.1038/35057062, 11237011.
3. Levy S, Sutton G, Ng P, Feuk L, Halpern A, Walenz B, Axelrod N, Huang J, Kirkness E, Denisov G, et al. The diploid genome sequence of an individual human. PLoS Biol 2007, 5(10):e254. 10.1371/journal.pbio.0050254, 1964779, 17803354.
4. Wheeler D, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen Y, Makhijani V, Roth G, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452(7189):872-876. 10.1038/nature06884, 18421352.
5. Pushkarev D, Neff N, Quake S. Single-molecule sequencing of an individual human genome. Nature biotechnology 2009, 27(9):847-850. 10.1038/nbt.1561, 19668243.
6. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, et al. The diploid genome sequence of an Asian individual. Nature 2008, 456(7218):60-65. 10.1038/nature07484, 2716080, 18987735.
7. Bentley D, Balasubramanian S, Swerdlow H, Smith G, Milton J, Brown C, Hall K, Evers D, Barnes C, Bignell H, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456(7218):53-59. 10.1038/nature07517, 2581791, 18987734.
8. McKernan K, Peckham H, Costa G, McLaughlin S, Fu Y, Tsung E, Clouser C, Duncan C, Ichikawa J, Lee C, et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome research 2009, 19(9):1527. 10.1101/gr.091868.109, 2752135, 19546169.
9. Ahn S, Kim T, Lee S, Kim D, Ghang H, Kim D, Kim B, Kim S, Kim W, Kim C, et al. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome research 2009, 19(9):1622. 10.1101/gr.092197.109, 2752128, 19470904.
10. Kim J, Ju Y, Park H, Kim S, Lee S, Yi J, Mudge J, Miller N, Hong D, Bell C, et al. A highly annotated whole-genome sequence of a Korean individual. Nature 2009, 460(7258):1011-1015. 2860965, 19587683.
11. Drmanac R, Sparks A, Callow M, Halpern A, Burns N, Kermani B, Carnevali P, Nazarenko I, Nilsen G, Yeung G, et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 2010, 327(5961):78. 10.1126/science.1181498, 19892942.
12. Ley T, Mardis E, Ding L, Fulton B, McLellan M, Chen K, Dooling D, Dunford-Shore B, McGrath S, Hickenbotham M, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008, 456(7218):66-72. 10.1038/nature07485, 2603574, 18987736.
13. Mardis E, Ding L, Dooling D, Larson D, McLellan M, Chen K, Koboldt D, Fulton R, Delehaunty K, McGrath S, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. New England Journal of Medicine 2009, 361(11):1058. 10.1056/NEJMoa0903840, 19657110.
14. Pleasance E, Stephens P, O'Meara S, McBride D, Meynert A, Jones D, Lin M, Beare D, Lau K, Greenman C, et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 2010, 463:184-190. 10.1038/nature08629, 2880489, 20016488.
15. Pleasance E, Cheetham R, Stephens P, McBride D, Humphray S, Greenman C, Varela I, Lin M, Ordóñez G, Bignell G, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 2010, 463:191-196. 10.1038/nature08658, 20016485.
16. Clark M, Homer N, O'Connor B, Chen Z, Eskin A, Lee H, Merriman B, Nelson S. U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet 2010, 6:e1000832. 10.1371/journal.pgen.1000832, 2813426, 20126413.
17. Rhead B, Karolchik D, Kuhn R, Hinrichs A, Zweig A, Fujita P, Diekhans M, Smith K, Rosenbloom K, Raney B, et al. The UCSC genome browser database: update 2010. Nucleic Acids Res 2010, 38(Database issue):D613-D619. 10.1093/nar/gkp939, 2808870, 19906737.
18. Mungall C, Emmert D, et al. A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics 2007, 23(13):i337. 10.1093/bioinformatics/btm189, 17646315.
19. Hubbard T, Aken B, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, et al. Ensembl 2007. Nucleic acids research 2006,
20. Kent W, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A, et al. The human genome browser at UCSC. Genome research 2002, 12(6):996. 186604, 12045153.
21. Stein L, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich J, Harris T, Arva A, et al. The generic genome browser: a building block for a model organism system database. Genome research 2002, 12(10):1599. 10.1101/gr.403602, 187535, 12368253.
22. Karolchik D, Hinrichs A, Furey T, Roskin K, Sugnet C, Haussler D, Kent W. The UCSC Table Browser data retrieval tool. Nucleic acids research 2004, 32(Database Issue):D493. 10.1093/nar/gkh103, 308837, 14681465.
23. Giardine B, Riemer C, Hardison R, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome research 2005, 15(10):1451. 10.1101/gr.4086505, 1240089, 16169926.
24. Fielding R. Architectural Styles and the Design of Network-based Software Architectures. PhD thesis 2000, University of California.
25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078. 10.1093/bioinformatics/btp352, 2723002, 19505943.
26. Deelman E, Singh G, Su M, Blythe J, Gil Y, Kesselman C, Mehta G, Vahi K, Berriman G, Good J, et al. Pegasus: A framework for mapping complex scientific workflows onto distributed systems. Scientific Programming 2005, 13(3):219-237.
27. Dean J, Ghemawat S. MapReduce: Simplified data processing on large clusters. Communications of the ACM 2008, 51:107-113.
28. Chang F, Dean J, Ghemawat S, Hsieh W, Wallach D, Burrows M, Chandra T, Fikes A, Gruber R. Bigtable: A distributed storage system for structured data. ACM Transactions on Computer Systems (TOCS) 2008, 26(2):4.
29. Langmead B, Schatz M, Lin J, Pop M, Salzberg S. Searching for SNPs with cloud computing. Genome Biology 2009, 10(11):R134. 10.1186/gb-2009-10-11-r134, 19930550.
30. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 2010,