String matching in hardware using the FM-Index

Proceedings - IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2011

Volumn , Issue , 2011, Pages 218-225

  Fernandez, Edward ^a   Najjar, Walid ^a   Lonardi, Stefano ^a  

^a University of California Riverside   (United States)

Author keywords

FPGA; Reconfigurable Computing; String matching

Indexed keywords

BOW TIE; BRUTE FORCE; BURROWS WHEELER TRANSFORM; EXACT-PATTERN MATCHING; FM-INDEX; FPGA-BASED HARDWARE IMPLEMENTATION; GENOME ANALYSIS; ORDERS OF MAGNITUDE; PACKET ROUTING; RECONFIGURABLE COMPUTING; SOFTWARE TOOL; STRING MATCHING; SUFFIX ARRAYS; SUFFIX-TREES; WEB QUERYING;

COMPUTER HARDWARE; DATA STRUCTURES; DNA SEQUENCES; FIELD PROGRAMMABLE GATE ARRAYS (FPGA); GENES; HARDWARE; INDEXING (OF INFORMATION); INTRUSION DETECTION; METADATA; UBIQUITOUS COMPUTING; USER INTERFACES;

PATTERN MATCHING;

EID: 79958698472     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/FCCM.2011.55     Document Type: Conference Paper

References (17)

1. M. Burrows and D.J. Wheeler, "A Block-sorting Lossless Data Compression Algorithm," SRC Research Report, May, 1994.
2. U. Manber and G. Myers, "Suffix Arrays: A New method for On-line String Searches," SIAM Journal of Computing, pp. 935-948. 1993.
3. st IEEE Symposium on Foundations of Computer Science, pp. 390-398, 2000.
4. th ACM-SIAM Symposium on Discrete Algorithms, pp. 269-278, 2001.
5. S. Grabowski, G. Navarro, R. Przywarski, A. Salinger and V. Makinen, "A Simple Alphabet-Independent FM-Index," International Journal of Foundations of Computer Science, Vol. 17, No. 6, pp. 1365-1384, 2006. (Pubitemid 44924925)
6. th European Conference on IR Research, pp. 113-123, 2007.
7. th IEEE International Conference on High Performance Computing and Communications, 2008.
8. J. Martinez, R. Cumplido, and C. Feregrino, "An FPGA-based Parallel Sorting Architecture for the Burrows-Wheeler Transform," In Proceedings of International Conference on Reconfigurable Computing and FPGAs", 2005.
9. th IEEE Workshop on Rapid System Prototyping, pp. 58, 2001.
10. P. Szecowka and T. Mandrysz, "Towards Hardware Implementation of BZIP2 Data Compression Algorithm," In Proceedings of Mixed Design of Integrated Circuits and Systems, pp. 337-340, 2009.
11. th International Conference on Field Programmable Logic and Application, 2010.
12. B. Langmead, C. Trapnell, M. Pop, and S. Salzberg, "Ultrafast and Memory-Efficient Alignment of Short DNA sequences to the Human Genome," Genome Biology, 2009.
13. H. Li and R. Durbin, "Fast and Accurate Short Read Alignment with Burrows-Wheeler Transforms," Bioinformatics, 2009.
14. R. Li, C. Yu, Y. Li, T. Lam, S. Yiu, K. Kristiansen, and J. Wang, "SOAP2: An Improved Ultrafast Tool for Short Read Alignment," Bioinformatics, 2009.
15. A. Apostolico and W. Szpankowski, Self-alignments in words and their applications, Journal of Algorithms, Volume 13, Issue 3, September 1992.
16. A. Aho and M. Corasick. Efficient String Matching: An Aid to Bibliographic Search. Communication of the ACM, June Vol. 18, No. 6, pp330-340, 1975.
17. D. Knuth, J. Morris, and V. Pratt, "Fast Pattern Matching in Strings," SIAM Journal of Computing, 1977.