Details

Title

Measurement Aspects of Genome Pattern Investigations - Hardware Implementation

Journal title

Metrology and Measurement Systems

Yearbook

2012

Numer

No 1

Publication authors

Divisions of PAS

Nauki Techniczne

Publisher

Polish Academy of Sciences Committee on Metrology and Scientific Instrumentation

Date

2012

Identifier

ISSN 0860-8229

References

GenBank (2010). <a target="_blank" href='http://www.ncbi.nlm.nih.gov/'>[PUBMED]</a> ; Pułka A. (2008), A New Hardware Algorithm for Searching Genome Patterns, null, 177. ; Milik A. (2011), On Efficient Implementation of Search for Genome Patterns, PAK, 57, 1, 15. ; 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 ; Yamaguchi Y. (2002), High Speed Homology Search with FPGAs, null, 271. ; Zhang F. (2002), A Parallel Smith-Waterman Algorithm Based on Divide and Conquer, null, 162. ; Benkrid K. (2007), High Performance Biosequence Database Scanning Using FPGAs, null, 361. ; Xilinx, The official Web site of the Xilinx Company <a target="_blank" href='http://www.xilinx.com/'>http://www.xilinx.com/</a> ; Zieliński M. (2009), Review of Single-Stage Time-Interval Measurement Modules Implemented in FPGA Devices, Metrology and Measurement Systems, 16, 4, 641. ; Ming Zhang (2010), DSP-FPGA Based Real-Time Power Quality Disturbances Classifier, Metrology and Measurement Systems, 17, 2, 205. ; Buyukkurt B. (2008), Compiler generated systolic arrays for wavefront algorithm acceleration on FPGAs, null, 655. ; Ashenden P. (2008), Digital Design - An Embedded Systems Approach Using VERILOG. ; Oliver T. (2004), High Performance Biosequence Database Scanning on Reconfigurable Platforms, null, 192. ; Lipton R. (1985), A systolic array for rapid string comparison, null, 363. ; Hoang. D. T. (1992). A Systolic Array for the Sequence Alignment Problem. <i>Brown University, Providence, RI, Technical Report CS-92-22</i>. ; Li T. (2007), 160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA), BMC Bioinformatics, 8. ; Hai Xu (2008), Improving Sequence Alignment using Class-Specific Score Matrices, null, 70. ; FASTA (2011). Sequence comparison at the University of Virginia. <a target="_blank" href='http://fasta.bioch.virginia.edu/'>http://fasta.bioch.virginia.edu/</a> ; BLAST (2011). Basic Local Alignment Search Tool. <a target="_blank" href='http://blast.ncbi.nlm.nih.gov/Blast.cgi'>[PUBMED]</a> ; Manavski S. (2008), CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment, BMC Bioinformatics, 9, 2. ; Liu Y. (2009), CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units, BMC Research Notes, 2, 73, doi.org/10.1186/1756-0500-2-73

DOI

10.2478/v10178-012-0004-0

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