FPGA-based scalable implementation of the general smith-waterman algorithm

Proceedings of the IASTED International Conference on Parallel and Distributed Computing and Systems

Volumn 16, Issue , 2004, Pages 410-415

  Cret, Octavian ^a   Mathe, Stefan ^a   Szente, Balint ^b   Mathe, Zsolt ^a   Vancea, Cristian ^a   Rusu, Florin ^a   Dǎrǎbant, Adrian ^c  

^a TECHNICAL UNIVERSITY OF CLUJ NAPOCA   (Romania)

^b UNIVERSITY OF MEDICINE AND PHARMACY   (Romania)

^c BABE BOLYAI UNIVERSITY   (Romania)

Author keywords

Bioinformatics; FPGA; Smith waterman algorithm; Systolic architecture; VHDL

Indexed keywords

ALGORITHMS; COMPUTER ARCHITECTURE; COMPUTER HARDWARE; MATHEMATICAL MODELS; PATTERN MATCHING; PROBLEM SOLVING;

BIOINFORMATICS; SMITH-WATER ALGORITHMS; SYSTOLIC ARCHITECTURES; VHDL;

FIELD PROGRAMMABLE GATE ARRAYS;

EID: 11844253174     PISSN: 10272658     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (6)

1. T. F. Smith and M. S. Waterman, Identification of common molecular subsequence, Journal of Molecular Biology, 147, 1951, 196-197.
2. National Center for Biotechnology Information. NCBI BLAST home page, 2003. http://www.ncbi.nlm.nih.gov/blast.
3. European Bioinformatics Institute Home Page, FASTA searching program, 2003. http://www.ebi.ac.uk/fasta33/.
4. th Conference on Field-Programmable Logic and Applications (FPL2003), Lisbon, 2003, 375-384.
5. Steven A. Guccione and Eric Keller, Gene matching using JBits, 2002. http://www.ccm.ece.vt.edu/hokiegene/papers/GeneMatchi ng.pdf.
6. R. Lipton and D. Lopresti, A systolic array for rapid string comparison, Proceedings of the Chapel Hill Conference on VLSI, pages 363-376, 1985.