CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

BMC Bioinformatics

Volumn 9, Issue SUPPL. 2, 2008, Pages

  Manavski, Svetlin A ^a,b   Valle, Giorgio ^a  

^a UNIVERSITY OF PADOVA   (Italy)

^b Elaide   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL COSTS; COMPUTATIONAL POWER; GRAPHICS PROCESSING UNIT; HARDWARE ACCELERATORS; REDUCED SENSITIVITY; SEQUENCE ALIGNMENTS; SINGLE INSTRUCTION MULTIPLE DATA; SMITH-WATERMAN ALGORITHM;

COMPUTER GRAPHICS; COMPUTER GRAPHICS EQUIPMENT; DNA SEQUENCES; HEURISTIC METHODS; MICROPROCESSOR CHIPS; MOLECULAR BIOLOGY; PROGRAM PROCESSORS; PROTEINS; SMART CARDS;

HARDWARE;

DNA; PROTEIN;

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ARTICLE; COMPUTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER PROGRAM; FINANCIAL MANAGEMENT; INFORMATION PROCESSING; INTERMETHOD COMPARISON; INTERNET; MATHEMATICAL ANALYSIS; MOLECULAR BIOLOGY; PROTEIN DATABASE; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; EQUIPMENT; EQUIPMENT DESIGN; INFORMATION RETRIEVAL; INSTRUMENTATION; METHODOLOGY; SIGNAL PROCESSING;

COMPUTER GRAPHICS; EQUIPMENT DESIGN; EQUIPMENT FAILURE ANALYSIS; INFORMATION STORAGE AND RETRIEVAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 43349092363     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S2-S10     Document Type: Article

References (16)

1. Pearson WR Lipman DJ Improved tools for biological sequence comparison Proc Natl Acad Sci U S A 1988, 85:2444-2448. 10.1073/pnas.85.8.2444 3162770 280013
2. Altschul SF Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25:3389-3402. 146917 9254694 10.1093/nar/25.17.3389
3. Farrar M Striped Smith-Waterman speeds database searches six times over other SIMD implementations Bioinformatics 2007, 23(2):156-161. 10.1093/ bioinformatics/btl582 17110365
4. Liu W Schmidt B Voss G Schroeder A Muller-Wittig W Bio-Sequence Database Scanning On GPU Proceeding of the 20th IEEE International Parallel & Distributed Processing Symposium: 2006(IPDSP 2006) (HICOMB Workshop Rhode Island, Greece; 2006.
5. Smith TF Waterman MS Identification of common molecular subsequences J Mol Biol 1981, 147:195-197. 10.1016/0022-2836(81)90087-5 7265238
6. Gotoh O An improved algorithm for matching biological sequences J. Mol. Biol 1982, 162:705-708. 10.1016/0022-2836(82)90398-9 7166760
7. NVidia CUDA [http://developer.NVidia.com/object/cuda.html]
8. AMD CTM [http://ati.amd.com/products/streamprocessor/index.html]
9. Rognes T Seeberg E Six-fold speed-up of Smith-waterman sequence database searches using parallel processing on common microprocessors Bioinformatics 2000, 16:699-706. 10.1093/bioinformatics/16.8.699 11099256
10. Chao KM Hardison RC Miller W Recent developments in linear-space alignment methods: A survey J. Comput. Biol 1994, 4:271-291.
11. Gribskov M McLachlan AD Eisenberg D Profile analysis: Detection of distantly related proteins Proc Natl Acad Sci U S A 1987, 84:4355-4358. 10.1073/pnas.84.13.4355 3474607 305087
12. Henikoff S Henikoff JG Amino acid substitution matrices from protein blocks Proc Natl Acad Sci U S A 1992, 89:10915-10919. 10.1073/ pnas.89.22.10915 1438297 50453
13. Needleman SB Wunsch CD A general method applicable to the search for similarities in the amino acid sequence of two proteins J. Mol. Biol 1970, 48:443-453. 10.1016/0022-2836(70)90057-4 5420325
14. Pearson W Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms Genomics 1991, 11:635-650. 10.1016/0888-7543(91)90071-L 1774068
15. Pearson W Rapid and sensitive sequence comparison with FASTP and FASTA Methods Enzymol 1990, 183:63-98. 2156132
16. Bairoch A Apweiler R The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 Nucleic Acids Res 2000, 28:45-48. 102476 10592178 10.1093/nar/28.1.45