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Visualization of Genome Signatures of Eukaryote Genomes by Batch-Learning Self-Organizing Map with a Special Emphasis on Drosophila Genomes
Joint Authors
Hamano, Yuta
Ikemura, Toshimichi
Abe, Takashi
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-8, 8 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-03-11
Country of Publication
Egypt
No. of Pages
8
Main Subjects
Abstract EN
A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods.
We previously established a sequence alignment-free clustering method “BLSOM” for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species.
In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available.
BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species.
In our detailed examination of 12 Drosophila species, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.
American Psychological Association (APA)
Abe, Takashi& Hamano, Yuta& Ikemura, Toshimichi. 2014. Visualization of Genome Signatures of Eukaryote Genomes by Batch-Learning Self-Organizing Map with a Special Emphasis on Drosophila Genomes. BioMed Research International،Vol. 2014, no. 2014, pp.1-8.
https://search.emarefa.net/detail/BIM-513732
Modern Language Association (MLA)
Abe, Takashi…[et al.]. Visualization of Genome Signatures of Eukaryote Genomes by Batch-Learning Self-Organizing Map with a Special Emphasis on Drosophila Genomes. BioMed Research International No. 2014 (2014), pp.1-8.
https://search.emarefa.net/detail/BIM-513732
American Medical Association (AMA)
Abe, Takashi& Hamano, Yuta& Ikemura, Toshimichi. Visualization of Genome Signatures of Eukaryote Genomes by Batch-Learning Self-Organizing Map with a Special Emphasis on Drosophila Genomes. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-8.
https://search.emarefa.net/detail/BIM-513732
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-513732