A new hardware architecture for genomic and proteomic sequence alignment

Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Volumn , Issue , 2004, Pages 730-731

  Knowles, Greg ^a   Gardner Stephen, Paul ^a  

^a FLINDERS UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTER ARCHITECTURE; COMPUTER HARDWARE; COMPUTER SOFTWARE; DATABASE SYSTEMS; DYNAMIC PROGRAMMING; FIELD PROGRAMMABLE GATE ARRAYS; GENES; MICROPROCESSOR CHIPS;

GENOMIC DATABASES; HARDWARE ARCHITECTURE; HOMOLOGY; PROTEOMIC SEQUENCES;

PROTEINS;

EID: 14044255863     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (10)

1. D.T Hoang, "Searching Genetic Databases on Splash 2", Proc. IEEE Workshop on FPGAs for Custom Computing, IEEE CS, 1993, pp. 185-191.
2. P. Guerdoux-Jamet, D. Lavenier, "SAMBA:Hardware Accelerator for Biological Sequence Comparison", CABIOS 12(6), pp. 609-615.
3. S.A. Guccione, E. Keller, "Gene Matching using JBITS", Proc. 12th Int. Workshop on Field-Programmable Logic and Applications (FPL'99), Springer, LNCS 2438, 2002, pp. 1168-1171.
4. B. Schmidt, H. Schroeder, M. Schimmler, "Massively Parallel Solutions for Molecular Sequence Analysis", Proc. 1st IEEE Int. Workshop on High Performance Computational Biology, Ft. Lauderdale, Florida, 2002.
5. T. Oliver, B. Schmidt, "High Performance Biosequence Database Scanning on Reconfigurable Platforms", Preprint, 2004.
6. C.W. Yu, K.H. Kwong, K.H. Lee, P.H.W. Leong, "A Smith-Waterman Systolic Cell", Proc. 13th Workshop on Field Programmable Logic and Applications (FPL'03), Springer, LNCS 2778, 2003, pp. 375-384.
7. TimeLogic Corporation, http://mm.timelogic.com
8. P. Gardner-Stephen, G. Knowles, "DASH: A New High Speed Genomic Search and Alignment Tool", 4th International Conference on Mathematics and Computers in Biology and Chemistry (MCBC 03),1, 2003, pp. 121-127.
9. P. Gardner-Stephen, G. Knowles, "DASH: Localising Dynamic Programming for Order of Magnitude Faster, Accurate Sequence Alignment", 3rd IEEE Computational Systems Bioinformatics Conference, Stanford, 2003.
10. Stephen F. Altschol et al, "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25, 1997, pp. 3389-3402.