Details

Title

An Efficient Hardware Implementation of Smith-Waterman Algorithm Based on the Incremental Approach

Journal title

International Journal of Electronics and Telecommunications

Yearbook

2011

Volume

vol. 57

Issue

No 4

Authors

Divisions of PAS

Nauki Techniczne

Publisher

Polish Academy of Sciences Committee of Electronics and Telecommunications

Date

2011

Identifier

DOI: 10.2478/v10177-011-0069-9 ; eISSN 2300-1933 (since 2013) ; ISSN 2081-8491 (until 2012)

Source

International Journal of Electronics and Telecommunications; 2011; vol. 57; No 4

References

GenBank. (2011) The official web of national center for biotechnology information. [Online]. Available: <a target="_blank" href='http://www.ncbi.nlm.nih.gov/'>[PUBMED]</a> ; Pettersson E. (2009), Generations of sequencing technologies, Genomics, 93, 105, doi.org/10.1016/j.ygeno.2008.10.003 ; Xu H. (2008), Improving sequence alignment using class-specific score matrices, null, 70. ; Gusfield D. (1997), Algorithms on strings, trees and sequences, doi.org/10.1017/CBO9780511574931 ; Smith T. (1981), Identification of common molecular sub-sequences, Journal of Molecular Biology, 147, 195, doi.org/10.1016/0022-2836(81)90087-5 ; FASTA. (2011) Sequence comparison at the university of virginia. [Online]. Available: <a target="_blank" href='http://fasta.bioch.virginia.edu/'>http://fasta.bioch.virginia.edu/</a> ; Herbordt M. (2006), Single pass, blast-like, approximate string matching on fpgas, null, 217. ; Liu Y. (2009), Cudasw++: optimizing smith-waterman sequence database searches for cuda-enabled graphics processing units, BMC Research Notes, 2, 1, 73, doi.org/10.1186/1756-0500-2-73 ; Manavski S. (2008), Cuda compatible gpu cards as efficient hardware accelerators for smith-waterman sequence alignment, BMC Bioinformatics. ; Benkrid K. (2007), High performance biosequence database scanning using fpgas, Processing of 2007 ICASSP, IEEE International Conference on Acoustics, Speech and Signal, 1, 361. ; Buyukkurt B. (2008), Compiler generated systolic arrays for wavefront algorithm acceleration on fpgas, null, 655. ; Li I. (2007), 160-fold acceleration of the smithwaterman algorithm using a field programmable gate array (fpga), BMC Bioinformatics, 8, 185, doi.org/10.1186/1471-2105-8-185 ; Oliver T. (2004), High performance biosequence database scanning on reconfigurable platforms, null, 192. ; Yamaguchi Y. (2002), High speed homology search with fpgas, null, 271. ; Hireche N. (2007), A systolic array for sequence comparison based on two-logic-levels processing element, null, 73. ; Lipton R. (1985), A systolic array for rapid string comparison, null, 363. ; Sastry R. (1993), A systolic array for approximate string matching, null, 402. ; Zhang F. (2002), A parallel smith-waterman algorithm based on divide and conquer, null, 162. ; TimeLogic. (2011) Decypher fpga biocomputing systems. [Online]. Available: <a target="_blank" href='http://www.timelogic.com/'>http://www.timelogic.com/</a> ; Xilinx. (2011) The official web site of the xilinx company. [Online]. Available: <a target="_blank" href='http://www.xilinx.com/'>http://www.xilinx.com/</a> ; Milik A. (2010), Hardware oriented optimization of smithwaterman algorithm, null, 319. ; Dydel S. (2006), Enabling reconfigurable hardware accelerators for the grid, null, 145. ; Phoophakdee B. (2007), Genome-scale disk-based suffix tree indexing, null, 833.
×