Classifying Nucleotide Sequences and their Positions of Influenza A Viruses through Several Kernels

Issei Hamada, Takaharu Shimada, Daiki Nakata, Kouichi Hirata, Tetsuji Kuboyama

2015

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.

Paper Citation

in Harvard Style

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, pages 342-347. DOI: 10.5220/0005251103420347

in Bibtex Style

@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},
}

in EndNote Style

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
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