Abstract
The effective comparison of biological data sequences is an important and a challenging task in bioinformatics. The sequence alignment process itself is a way of arranging DNA sequences in order to identify similar areas that may have a consequence of functional, structural or evolutionary relations between them. A new effective and unified method for sequence alignment on the basic of trilateration, called CAT method, and using C (cytosine), A (adenine) and T (thymine) benchmarks is presented in this paper. This method suggests solutions to three major problems in sequence alignment: creating a constant favorite sequence, reducing the number of comparisons with the favorite sequence, and unifying/standardizing the favorite sequence by defining benchmark sequences.
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References
Mount, D.: Bioinformatics: Sequence and Genome Analysis, 2nd edn. Cold Spring Harbor Laboratory Press, New York (2009)
Needleman, S., Wunsch, C.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453 (1970)
Smith, T., Waterman, M.: Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197 (1981)
Lipman, D.J., Pearson, W.R.: Rapid and sensitive protein similarity searches. Science 227(4693), 1435–1441 (1985). https://doi.org/10.1126/science.2983426. PMID 2983426
Altschul, S., et al.: Basic local alignment search tool. J. Mol. Biol. 215(3), 403–410 (1990)
Altschul, S., et al.: Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)
Lin, H., et al.: Efficient data access for parallel BLAST. In: 19th International Parallel & Distributed Processing Symposium (2005)
Zhang, F., Qiao, X.Z., Liu, Z.Y.: A parallel Smith-Waterman algorithm based on divide and conquer. In: Proceedings of the Fifth International Conference on Algorithms and Architectures for Parallel Processing ICA3PP 2002 (2002)
Farrar, M.: Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics 23(2), 156–161 (2007)
Borovska, P., Gancheva, V., Landzhev, N.: Massively parallel algorithm for multiple biological sequences alignment. In: Proceeding of 36th IEEE International Conference on Telecommunications and Signal Processing (2013). https://doi.org/10.1109/TSP.2013.6614014
Motlagh, O., Tang, S.H., Ismail, H., Ramli, A.R.: A review on positioning techniques and technologies: a novel AI approach. J. Appl. Sci. 9, 1601–1614 (2019). https://doi.org/10.3923/jas.2009.1601.1614
Thapa, K., Case, S.: An indoor positioning service for bluetooth ad hoc networks. In: Proceedings of the Midwest Instruction and Computing Symposium, 11–12 April 2003, Duluth, MN, USA, pp. 1–11 (2003)
Ciurana, M., Barcelo-Arroyo, F., Izquierdo, F.: A ranging system with IEEE 802.11 data frames. In: 2007 IEEE Radio and Wireless Symposium (2007). https://doi.org/10.1109/rws.2007.351785
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This work is supported by Grant DN07/24.
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Gancheva, V., Stoev, H. (2019). DNA Sequence Alignment Method Based on Trilateration. In: Rojas, I., Valenzuela, O., Rojas, F., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2019. Lecture Notes in Computer Science(), vol 11466. Springer, Cham. https://doi.org/10.1007/978-3-030-17935-9_25
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DOI: https://doi.org/10.1007/978-3-030-17935-9_25
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