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Authors: Issei Hamada 1 ; Takaharu Shimada 1 ; Daiki Nakata 1 ; Kouichi Hirata 1 and Tetsuji Kuboyama 2

Affiliations: 1 Kyushu Institute of Technology, Japan ; 2 Gakushuin University, Japan

Keyword(s): Kernels, Nucleotide Sequences, Positions in Nucleotide Sequences, Phylogenetic Trees.

Related Ontology Subjects/Areas/Topics: Applications ; Bioinformatics and Systems Biology ; Kernel Methods ; Pattern Recognition ; Software Engineering ; Theory and Methods

Abstract: In this paper, we classify nucleotide sequences and their positions of influenza A viruses by using both nucleotide sequence kernels and phylogenetic tree kernels. In the nucleotide sequence kernel, we regard a nucleotide sequence as a vector, a multiset and a string. In the phylogenetic tree kernel, we use a relabeled phylogenetic tree obtained by replacing the labels of leaves that are indices of nucleotide sequences in the reconstructed phylogenetic tree from a set of nucleotide sequences with the nucleotides at a fixed position and trimmed phylogenetic trees obtained by trimming the branches in the relabeled phylogenetic tree with same leaves as possible. Then, we observe which of kernels are effective the classification of nucleotide sequences as analyzing pandemic occurrences and regions and the classification of positions in nucleotide sequences as analyzing positions in packaging signals.

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Paper citation in several formats:
Hamada, I.; Shimada, T.; Nakata, D.; Hirata, K. and Kuboyama, T. (2015). Classifying Nucleotide Sequences and their Positions of Influenza A Viruses through Several Kernels. In Proceedings of the International Conference on Pattern Recognition Applications and Methods - Volume 1: ICPRAM; ISBN 978-989-758-076-5; ISSN 2184-4313, SciTePress, pages 342-347. DOI: 10.5220/0005251103420347

@conference{icpram15,
author={Issei Hamada. and Takaharu Shimada. and Daiki Nakata. and Kouichi Hirata. and Tetsuji Kuboyama.},
title={Classifying Nucleotide Sequences and their Positions of Influenza A Viruses through Several Kernels},
booktitle={Proceedings of the International Conference on Pattern Recognition Applications and Methods - Volume 1: ICPRAM},
year={2015},
pages={342-347},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005251103420347},
isbn={978-989-758-076-5},
issn={2184-4313},
}

TY - CONF

JO - Proceedings of the International Conference on Pattern Recognition Applications and Methods - Volume 1: ICPRAM
TI - Classifying Nucleotide Sequences and their Positions of Influenza A Viruses through Several Kernels
SN - 978-989-758-076-5
IS - 2184-4313
AU - Hamada, I.
AU - Shimada, T.
AU - Nakata, D.
AU - Hirata, K.
AU - Kuboyama, T.
PY - 2015
SP - 342
EP - 347
DO - 10.5220/0005251103420347
PB - SciTePress