Exact and complete short-read alignment to microbial genomes using graphics processing unit programming

Bioinformatics

Volumn 27, Issue 10, 2011, Pages 1351-1358

  Blom, Jochen ^a   Jakobi, Tobias ^a   Doppmeier, Daniel ^a   Jaenicke, Sebastian ^a   Kalinowski, Jörn ^a   Stoye, Jens ^a   Goesmann, Alexander ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BACTERIAL GENOME; BIOLOGY; COMPUTER PROGRAM; DNA SEQUENCE; GENE EXPRESSION PROFILING; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT;

ALGORITHMS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENOME, BACTERIAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 79955767858     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr151     Document Type: Article

References (17)

1. Burrows,M. and Wheeler,D.J. (1994) A block-sorting lossless data compression algorithm. Technical Report 124, Digital Systems Research Center, Palo Alto, California.
2. Califano,A. and Rigoutsos,I. (2002) FLASH: A fast look-up algorithm for string homology. In Computer Vision and Pattern Recognition, 1993. Proceedings CVPR'93., 1993 IEEE Computer Society Conference on. IEEE, New York, NY, USA, pp. 353-359.
3. Campagna,D. et al. (2009) PASS: a program to align short sequences. Bioinformatics, 25, 967.
4. Farrar,M. (2007) Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics, 23, 156-161.
5. Jokinen,P. and Ukkonen,E. (1991) Two algorithms for approximate string matching in static texts. Lecture Notes in Computer Science, 520/1991, 240-248.
6. Langmead,B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
7. Liu,W. et al. (2006) Bio-sequence database scanning on a GPU. In Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International, IEEE, Rhodes Island, Greece, p. 8.
8. Liu,Y. et al. (2009) CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Res. Notes, 2, 73.
9. Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
10. Li,H. et al. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
11. Li,R. et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
12. Manavski,S.A. and Valle,G. (2008) CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics, 9 (Suppl. 2), S10.
13. Needleman,S.B. andWunsch,C.D. (1970)Ageneral method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
14. Rognes,T. and Seeberg,E. (2000) Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors. Bioinformatics, 16, 699-706.
15. Rumble,S. et al. (2009) SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol., 5, e1000386.
16. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
17. Szalkowski,A. et al. (2008) SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2. BMC Res. Notes, 1, 107.