Abstract
In this paper we present an application of the neural gas network to the classification of the DNA barcode sequences. The proposed method is based on the identification of distinctive words, extracted from the spectral representation of DNA sequences. In particular we calculated the “signatures” that are a characteristic of the DNA sequence at different taxonomic levels. In order to demonstrate the efficacy of the proposed method, we tested it over 10 real barcode datasets belonging to different animalia species, provided by on-line resource Barcode of Life Database (BOLD).
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Alberg, A.J., Park, J.W., Hager, B.W., Brock, M.V., Diener-West, M.: The use of “overall accuracy” to evaluate the validity of screening or diagnostic tests. Journal of General Internal Medicine 5(pt. 1), 460–465 (2004)
Chan, C.K.K., Hsu, A.L., Tang, S.L., Halgamuge, S.K.: A Method for Evaluating Quality of Clustering DNA Fragments Encoded in Different Nucleotide Frequencies. In: Proceeding of FBIT 2007, pp. 60–63. IEEE (2007)
Chor, B., Horn, D., Goldman, N., Levy, Y., Massingham, T.: Genomic DNA k-mer spectra: models and modalities. Genome Biology 10(10), R108 (2009)
Cottrell, M., Hammer, B., Hasenfuss, A., Villmann, T.: Batch and median neural gas. Neural Networks 19(6-7), 762–771
Fiannaca, A., Di Fatta, G., Rizzo, R., Urso, A., Gaglio, S.: Simulated annealing technique for fast learning of SOM networks. Neural Computing and Applications (2011)
Hebert, P.D.N., Ratnasingham, S., DeWaard, J.R.: Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society. Series B, Biological sciences 270(suppl.), S96–S99 (2003)
Jaccard, P.: Nouvelles recherches sur la distribution florale. Bul. Soc. Vaudoise Sci. Nat. 44, 223–270 (1908)
Kuksa, P., Pavlovic, V.: Efficient alignment-free DNA barcode analytics. BMC Bioinformatics 10(suppl. 14), S9 (2009)
La Rosa, M., Fiannaca, A., Rizzo, R., Urso, A.: Alignment-free Analysis of Barcode Sequences by means of Compression-Based Methods. BMC Bioinformatics 14 (suppl. 7), S4 (2013)
Leisch, F.: A toolbox for -centroids cluster analysis. Computational Statistics & Data Analysis 51(2), 526–544 (2006)
Martinetz, T.M., Berkovich, S.G., Schulten, K.J.: “Neural-gas” network for vector quantization and its application to time-series prediction. IEEE Transactions on Neural Networks 4(4), 558–569 (1993)
Ratnasingham, S., Hebert, P.D.N.: bold: The Barcode of Life Data System. Molecular Ecology Notes 7(3), 355–364 (2007), http://www.barcodinglife.org
Seiffert, U., Hammer, B., Kaski, S., Villmann, T.: Neural networks and machine learning in bioinformatics-theory and applications. In: European Symposium on Artificial Neural Networks, pp. 521–532 (2006)
Vinga, S., Almeida, J.: Alignment-free sequence comparison–a review. Bioinformatics 19(4), 513–523 (2003)
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Fiannaca, A., La Rosa, M., Rizzo, R., Urso, A. (2013). Analysis of DNA Barcode Sequences Using Neural Gas and Spectral Representation. In: Iliadis, L., Papadopoulos, H., Jayne, C. (eds) Engineering Applications of Neural Networks. EANN 2013. Communications in Computer and Information Science, vol 384. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-41016-1_23
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DOI: https://doi.org/10.1007/978-3-642-41016-1_23
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