MULTIHEURISTIC APPROACH TO COMPARE THE QUALITY OF DEFINED METRICS ON THE SET OF DNA SEQUENCES
Abstract
In this article, we analyzed some several metrics that determine the differences in DNA sequences of different species. Several standard metrics are considered, as well as a modification of the original author's metric, the previous versions of which were considered in our previous publications. Determining the quality of some several metrics, we proceed from the assumption that for any three distant species, the distances between them computed from this metric should form a triangle close to an isosceles acute-angled triangle. We consider several variants of the deviation of a triangle from an isosceles acute-angled triangle, and then we consider the sum of such deviations for all the resulting triangles. Based on these calculations, we make a conclusion about the quality of the original metrics. After these calculations, we apply the obtained technique to the consideration of the same metrics for close species (anthropoid and human), and on these closely related species, we obtain slightly different results of a comparative analysis of the metrics under consideration.
References
2. Toppi, J., De VicoFallani, F.,Petti, M., Veссhiato, G., Maglione, A. G., Cincotti, F., Salinari, S., Mattia, D., Babiloni, F., Astolfi, L. (2013), “A new statistical approach for the extraction of adjacency matrix from effective connectivity networks”, “IEEE Engineering in Medicine and Biology Society (EMBC)”, No 3-7, pp. 2932-2935.
3. Torshin, I. Yu. (2006), “Bioinformatics in the Post-Genomic Era: The Role of Biophysics”, Nova Biomedical Books, NY,ISBN 1-60021-048-1.
4. Winkler, W. E. (1990), String Comparator Metrics and Enhanced Decision Rules in the Fellegi-Sunter Model of Record Linkage, Proceedings of the Survey Research Methods Sections, American Statistical Association, pp. 354-359.
5. Van der Loo, M. P. J. (2014), “The Stringdist Package for Approximate String Matching”,The R Journal, vol. 6, pp. 111-122.
6. Pages, H., Aboyoun, P., Gentleman, R., DebRaoy, S. (2009), “Biostrings: String Objects Representing Biological Sequences and Matching Algorithms”, R package version 2.10.1.
7. Morgan, M., Lawrence, M. (2009), “ShortRead: Base classes and methods for high-throughput short-read sequencing data”, R package version 1.0.6.
8. Melnikov, B. F., (2006) “Multiheuristic approach to discrete optimization problems”, Cybernetics and Systems Analysis, No. 3, pp. 335-341.
9. Melnikov, B.F. (2005), “Discrete optimization problems some new heuristic approaches”, Proceedings – Eighth International Conference on High-Performance Computing in Asia-Pacific Region, HPC Asia 2005 8th International Conference on High-Performance Computing in Asia-Pacific Region, China Computer Federation, Beijing, pp. 73-80.
10. Makarkin, S., Melnikov, B., PaninА. (2013), “On the metaheuristics approach to the problem of genetic sequence comparison and its parallel implementation”, Applied Mathematics (Scientific Research Publishing), Vol. 04, No. 10, pp. 35-39.
11. Eckes, B.,Nischt, R.,Krieg, T. (2010), “Cell-matrix interactions in dermal repair and scarring”, Fibrogenesis Tissue Repair., No. 3:4, doi:10.1186/1755-1536-3-4.
12. Carr R.W., HennessyJ. L., (1981),“WSCLOCK – a simple and effective algorithm for virtual memory management”, SOSP '81 Proceedings of the eighth ACM symposium on Operating systems principles, pp. 87-95.
13. Melnikov, B.F. (2001), “Heuristics in programming of nondeterministic games”, Programming and Computer Software., No. 5, pp. 277-288.
14. Melnikov, B., Radionov, A.,Moseev, A.,Melnikova, E., (2006),“Some specific heuristics for situation clustering problems”, ICSOFT, Technologies, Proceedings 1st International Conference on Software and Data Technologies, pp. 272-279.
15. Foley, J. (2011),”Fossil Hominids: mitochondrial DNA”, available at: http://www.talkorigins.org/faqs/homs/mtDNA.html
16. Frans, B. M., (1997), “Bonobo: The Forgotten Ape”, University of California Press, ISBN 0-520-20535-9; trade paperback, October, 1998, pp. 224.
17. Popkov , Y. S. (1995), “Substantiation of the entropy maximization method for problems of image restoration from projections”, Automation and Remote Control, 56:1, pp. 77-82.
18. (2014) NCBI:nucleotidedatabase,availableat:http://www.ncbi.nlm.nih.gov/nuccore.
19. Makarrin, S., Melnikov, B., (2013), “Geometricheskie metodi reshenia psevdogeometricheskoi versii zadachi kommiviashera”, Stohasticheskaia optimizacia v informatike, Т. 9., № 2., pp. 54-72.
20. Midwood, K. S., Williams, L. V., Schwarzbauer, J. E. (2004), “Tissue repair and the dynamics of the extracellular matrix”, The International Journal of Biochemistry & Cell Biology, Vol. 36, Issue 6, pp. 1031–1037
21. Shao, M., Lin, Y., Moret, B. , (2014), “An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes”, Research in Computational Molecular Biology, Lecture Notes in Computer Science Volume 8394, pp. 280-292.
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