Mapping uniquely occurring short sequences derived from high throughput technologies to a reference genome

Final Program and Abstract Book - 9th International Conference on Information Technology and Applications in Biomedicine, ITAB 2009

Volumn , Issue , 2009, Pages

  Antoniou, Pavlos ^a   Daykin, Jackie W ^b   Iliopoulos, Costas S ^b   Kourie, Derrick ^c   Mouchard, Laurent ^d   Pissis, Solon P ^b  

^a UNIVERSITY OF CYPRUS   (Cyprus)

^b KING'S COLLEGE LONDON   (United Kingdom)

^c UNIVERSITY OF PRETORIA   (South Africa)

^d UNIVERSITÉ DE ROUEN   (France)

Author keywords

High throughput; Mapping; Pattern matching; Sequencing; Short reads

Indexed keywords

EFFICIENT ALGORITHM; GENOME SEQUENCING; HIGH THROUGHPUT; HIGH THROUGHPUT TECHNOLOGY; LOWER COST; MAPPING PATTERN; PATTERN MATCHING PROBLEMS; PRACTICAL ALGORITHMS; SEQUENCING METHOD; SHORT SEQUENCES;

ALGORITHMS; GENES; INFORMATION TECHNOLOGY; MAPPING; PATTERN MATCHING;

THROUGHPUT;

EID: 77949634308     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ITAB.2009.5394394     Document Type: Conference Paper

References (19)

1. S. Bennett. Solexa ltd. Pharmacogenomics, 5(4):433-438, 2004.
2. T. H. Cormen, C. E. Leiserson, R. L. Rivest, and C. Stein. Introduction to Algorithms, Second Edition. The MIT Press, September 2001.
3. A. Cox. (unpublished) ELAND: Efficient local alignment of nucleotide data.
4. B. Dömölki. An algorithm for syntactic analysis. Computational Linguistics, 8:29-46, 1964.
5. N. Hall. Advanced sequencing technologies and their wider impact in microbiology. J. Exp. Biol., 210:1518-1525, 2007.
6. D. Hernandez, P. Francois, L. Farinelli, M. Osteras, and J. Schrenzel. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res, March 2008.
7. H. Jiang and W. H. Wong. Seqmap: mapping massive amount of oligonucleotides to the genome. Bioinformatics, 24(20):2395-2396, 2008.
8. R. M. Karp and M. O. Rabin. Efficient randomized pattern-matching algorithms. IBM J. Res. Dev., 31(2):249-260, 1987.
9. H. Li, J. Ruan, and R. Durbin. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research, 18(11):1851-1858, 2008.
10. R. Li, Y. Li, K. Kristiansen, and J. Wang. SOAP: short oligonucleotide alignment program. Bioinformatics, 24(5):713-714, 2008.
11. E. H. Margulies and E. Birney. Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes. Nat. Rev. Genet., 9:303-313, 2008.
12. O. Morozova and M. A. Marra. Applications of next-generation sequencing technologies in functional genomics. Genomics, 92(5):255-264, 2008.
13. A. Mortazavi, B. A. A. Williams, K. McCue, L. Schaeffer, and B. Wold. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods, May 2008.
14. J. M. Prober, G. L. Trainor, R. J. Dam, F. W. Hobbs, C. W. Robertson, R. J. Zagursky, A. J. Cocuzza, M. A. Jensen, and K. Baumeister. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science, 238:336-341, 1987.
15. F. Sanger and A. R. Coulson. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. BioI., 94:441-448, 1975.
16. F. Sanger, S. Nicklen, and A. R. Coulson. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA, 74:5463-5467, 1977.
17. S. C. Schuster. Next-generation sequencing transforms today's biology. Nat. Methods, 5:16-18, 2008.
18. L. M. Smith, J. Z. Sanders, R. J. Kaiser, P. Hughes, C. Dodd, C. R. Connell, C. Heiner, S. B. Kent, and L. E. Hood. Fluorescence detection in automated DNA sequence analysis. Nature, 321:674-679, 1986.
19. B. Wold and R. Myers. Sequence consensus methods for functional genomics. Nature Methods, 5(1):19-21, 2008.