Abstract
According to 2-D chaos game representation of RNA secondary structures, we propose a new method of 3-D graphical representation which does not lose any biological information. Then we extract a new numerical feature which called inner products from 3-D graphical representation. It is regarded as a value to analyze the relationship between nine kinds of viruses. We find that our conclusion is almost consistent with the reported data and the realities of life. Finally, we use the method of inter-class analysis to analyze our results. The works show that our data improve 7.52 % on interclass distance and about 7 % in different class. It is easier to distinguish the different classes than previous results.
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References
Sun, X., Lu, Z.H., Xie, J.M.: Bioinformatics Basis. Qinghua University Press, Beijing (2005)
Needleman, S.B., Wunsch, C.D.: 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.F., Waterman, M.S.: Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197 (1981)
Yao, Y.H., Dai, Q., Ling, L., Nan, X.Y., He, P.A., Zhang, Y.Z.: Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation. J. Com. Chem. 31, 1045–1052 (2010)
Liu, Z., Liao, B., Zhu, W., Huang, G.: A 2D graphical representation of DNA sequence based on dual nucleotides and its application. Int. J. Quantum Chem. 109, 948–958 (2009)
Yao, Y.H., Dai, Q., Nan, X.Y., He, P.A., Zhang, Y.Z.: Analysis of similarity/dissimilarity of DNA sequences base on a class of 2D graphical representation. J. Com. Chem. 29, 1632–1639 (2008)
Randic, M., Vracko, M., Lers, N.: Analysis of similarity/dissimilarity of DNA sequence base on novel 2D graphical representation. Chem. Phys. Lett. 371, 202–207 (2003)
Tang, X.C., Zhou, P.P., Qiu, W.Y.: On the similarity/dissimilarity of DNA sequences based on novel 4D graphical representation. Chinese. Sci. Bull. 55, 701–704 (2010)
Li, M., Badger, J.H., Chen, X., Kwong, S., Kearney, P., Zhang, H.Y.: An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 17, 149–154 (2001)
Wu, T.J., Hsiech, Y.C., Li, L.A.: Statistical measures of DNA sequence dissimilarity under Markov chain models of based composition. Biometrics. 57, 441–448 (2001)
Pham, T.D., Zuegg, J.: A probabilistic measure for alignment free sequence comparison. Bioinformatics 20, 3455–3461 (2004)
Jeong, B.S., Bari, A.G., Reaz, M.R., Jeon, S., Lim, C.G., Choi, H.J.: Codon-based encoding for DNA sequence analysis. Methods 67, 373–379 (2014)
Sczepansiky, J.T., Joyce, G.F.: A cross-chiral RNA polymerase ribozyme. Nature 515, 440–442 (2014)
Karunatilaka, K.S., Rueda, D.: Post-transcriptional modifications modulate conformational dynamics in human U2-U6 snRNA complex. RNA 20, 16–23 (2014)
Branddis, K.A., Gale, S., Jinn, S., et al.: Box C/D small nucleolar RNA (snoRNA) U60 regulates intracellular cholesterol trafficking. J. Mol. Biol. 288, 35703–35713 (2013)
Yao, Y.H., Wang, T.M.: A 2D graphical representation of RNA secondary structure and the analysis of similarity/dissimilarity based on it. J. Chem. 26, 1339–1346 (2005)
Zhang, Y., Qiu, J.: Comparing RNA secondary structures based on 2D graphical representation. Chem. Phys. Lett. 458, 180–185 (2008)
Liu, L.W., Wang, T.M.: On 3D graphical representation of RNA secondary structure and their applications. J. Mol. Biol. 42, 595–602 (2007)
Feng, J., Wang, T.M.: A 3D graphical representation of RNA secondary structure based on chaos games representation. Chem. Phys. Lett. 454, 355–361 (2008)
Bai, F.L., Li, D.C., Wang, T.M.: A new mapping rules for RNA secondary structures with its applications. J. Math. Chem. 43, 932–942 (2008)
Tian, F.C., Wang, S.Y., Wang, J., Liu, X.: Similarity analysis of RNA secondary structures with symbolic dynamics. J. Com. Res. Develop. 50, 445–452 (2013)
Guo, Y., Wang, T.M.: A new method to analyze the similarity of the DNA sequences. J. Mol. Struc-THEOCHEM 853, 62–67 (2008)
Wang, S.Y., Tian, F.C., Qiu, Y., Liu, X.: Bilateral similarity function: a novel and universal method for similarity analysis of biological sequences. J. Theor. Biol. 265, 194–201 (2010)
Liu, X., Tian, F.C., Wang, S.Y.: Analysis of similarity/dissimilarity of DNA sequences based on convolutional code model. Nucleos. Nucleot. Nucl. 29, 123–131 (2010)
Acknowledgement
This work is supported by the National Natural Science Foundation of China (Nos. 61425002, 61402066, 61402067, 31370778, 61370005, 31170797), the Basic Research Program of the Key Lab in Liaoning Province Educational Department (Nos. LZ2014049, LZ2015004), the Project Supported by Natural Science Foundation of Liaoning Province (No. 2014020132), the Project Supported by Scientific Research Fund of Liaoning Provincial Education (No. L2014499), and by the Program for Liaoning Key Lab of Intelligent Information Processing and Network Technology in University.
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Xing, S., Wang, B., Zhou, C., Zhang, Q. (2015). RNA Sequences Similarities Analysis by Inner Products. In: Bikakis, A., Zheng, X. (eds) Multi-disciplinary Trends in Artificial Intelligence. MIWAI 2015. Lecture Notes in Computer Science(), vol 9426. Springer, Cham. https://doi.org/10.1007/978-3-319-26181-2_31
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DOI: https://doi.org/10.1007/978-3-319-26181-2_31
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