Abstract
DNA sequences can be often showed in fragments, little pieces, found at crime scene or in a hair sample for paternity exam. In order to compare that fragments with a subject or target sequence of a suspect, we need an efficient tool to analyze the DNA sequence alignment and matching. So DNA matching is a bioinformatics field that could find relationships functions between sequences, alignments and them try to understand it. Usually done by software through databases clusters analysis, DNA matching requires a lot of computational resources, what may increase the bioinformatics project budget. We propose the approach of a hardware parallel architecture, based on heuristic method, capable of reducing time spent on matching process.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. J. Mol. Biol. 215(3), 403–410 (1990)
Baldi, P., Brunak, S.: Bioinformatics: the machine learning approach, 1st edn. MIT Press, Cambridge (2001)
Baxevanis, A.D., Francis Ouellette, B.F.: Bioinformatics: a practical guide to the analysis of genes and proteins, 1st edn. Wiley Interscience, Hoboken (1998)
Giegerich, R.: A systematic approach to dynamic programming in bioinformatics. Bioinformatics 16(8), 665–677 (2000)
Lipman, D.J., Pearson, W.R.: Rapid and sensitive protein similarity searches. Science 227(4693), 1435–1441 (1985)
ModelSim, High performance and capacity mixed HDL simulation, Mentor Graphics (2011), http://model.com
Mount, D.W.: Bioinformatics: sequence and genome analysis, 2nd edn. Cold Spring Harbor Laboratory Press (2004)
Navabi, Z.: VHDL: Analysis and modeling of digital systems, 2nd edn. McGraw Hill, New York (1998)
Needlman, S.B., Wunsh, S.B.: A general method applicable to the search of similarities in amino acid sequence of two protein. J. Mol. Biol. 48, 443–453 (1970)
Pearson, W.R., Lipman, D.J.: Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America 85(8), 2444–2448 (1988)
Pearson, W.: Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11(3), 635–650 (1991)
Pearson, W.: Comparison of methods for searching protein sequence databases. Protein Science 4(6), 1145 (1995)
Searls, D.: The language of genes, vol. 420, pp. 211–217 (2002)
Shpaer, E.G., Robinson, M., Yee, D., Candlin, J.D., Mines, R., Hunkapiller, T.: Sensitivity and selectivity in protein similarity searches: a comparison of Smith-Waterman in hardware to BLAST and FASTA. Genomics 38(2), 179–191 (1996)
Oehmen, C., Nieplocha, J.: ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis. IEEE Transactions on Parallel & Distributed Systems 17(8), 740–749 (2006)
Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. J. Mol. Biol. 147(1), 195–197 (1981)
Wolf, W.: FPGA-based system design. Prentice-Hall, Englewood Cliffs (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Segundo, E.J.G.N., Nedjah, N., de Macedo Mourelle, L. (2011). A Parallel Architecture for DNA Matching. In: Xiang, Y., Cuzzocrea, A., Hobbs, M., Zhou, W. (eds) Algorithms and Architectures for Parallel Processing. ICA3PP 2011. Lecture Notes in Computer Science, vol 7017. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-24669-2_38
Download citation
DOI: https://doi.org/10.1007/978-3-642-24669-2_38
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-24668-5
Online ISBN: 978-3-642-24669-2
eBook Packages: Computer ScienceComputer Science (R0)