Abstract
In this paper, first we introduce a label-based closest-neighbor trimming method to trim a phylogenetic tree built from nucleotide sequences according to the labels of leaves. Next, by replacing the indices of nucleotide sequences as labels of leaves with the nucleotides occurring in a position, we formulate a trim distance between two positions in nucleotide sequences as the LCA-preserving distance between the trimmed phylogenetic trees according to nucleotides occurring in the positions. Finally, we apply the trim distance to compare pandemic influenza A (H1N1) viruses with non-pandemic ones.
This work is partially supported by Grand-in-Aid for Scientific Research 22240010, 24300060 and 24700289 from the Ministry of Education, Culture, Sports, Science and Technology, Japan.
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References
Bao, T., Bolotov, P., Dernovoy, D., Kiryutin, B., Zaslavsky, L., Tatusova, T., Ostell, J., Lipman, D.: The influenza virus resource at the National Center for Biotechnology Information. J. Virol 82, 596–601, http://www.ncbi.nlm.gov/genomes/FLU/
Durbin, R., Eddy, S., Krogh, A., Mitchison, G.: Biological sequence analysis. Cambridge University Press (1998)
Kao, M.-Y., Lam, T.-W., Sing, W.-K., Ting, H.F.: An even faster and more unifying algorithm for comparing trees via unbalanced bipartite matchings. J. Algo. 40, 212–233 (2001)
Koperwas, J., Walczak, K.: Tree edit distance for leaf-labelled trees on free leafset and its comparison with frequent subsplit dissimilarity and popular distance measures. BMC Bioinformatics 12, 204 (2011)
Lu, S.-Y.: A tree-to-tree distance and its application to cluster analysis. IEEE Trans. Pattern Anal. Mach. Intell. 1, 219–224 (1979)
Sung, W.-K.: Algorithms in bioinformatics: A practical introduction. Champman and Hall/CRC (2009)
Yonezawa, K., Igarashi, M., Ueno, K., Takada, A., Ito, K.: The closest-neighbor trimming method: A resampling algorithm for nucleotide sequence datasets (submitted)
Zhang, K., Wang, J.T.L., Shasha, D.: On the editing distance between undirected acyclic graph. Int. J. Found. Comput. Sci. 7, 43–58 (1995)
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© 2012 Springer-Verlag Berlin Heidelberg
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Makino, S., Shimada, T., Hirata, K., Yonezawa, K., Ito, K. (2012). A Trim Distance between Positions in Nucleotide Sequences. In: Ganascia, JG., Lenca, P., Petit, JM. (eds) Discovery Science. DS 2012. Lecture Notes in Computer Science(), vol 7569. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33492-4_9
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DOI: https://doi.org/10.1007/978-3-642-33492-4_9
Publisher Name: Springer, Berlin, Heidelberg
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