Sequence alignment-free method for phylogenetic and functional prediction and its application to molecular evolutionary studies
| Project/Area Number |
18570216
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Evolutionary biology
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| Research Institution | Nagahama Institute of Bio-Science and Technology |
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Principal Investigator |
IKEMURA Toshimichi Nagahama Institute of Bio-Science and Technology, Faculty of Bio-Science, Professor (50025475)
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| Co-Investigator(Kenkyū-buntansha) |
ABE Takashi Nagahama Institute of Bio-Science and Technology, Faculty of Bio-Science, Assistant Professor (30390628)
洞田 慎一 総合研究大学院大学, 葉山高等研究センター, 上級研究員 (70377125)
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| Project Period (FY) |
2006 – 2007
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| Project Status |
Completed (Fiscal Year 2007)
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| Budget Amount *help |
¥4,020,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥420,000)
Fiscal Year 2007: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2006: ¥2,200,000 (Direct Cost: ¥2,200,000)
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| Keywords | Bioinformatics / Environmental microorganisms / SOM / Protein function prediction / Phylogenetic prediction / Self-Organizing Map / Earth Simulator / Methagenome / メタゲノム解析 / オリゴヌクレオチド頻度 / 自己組織化マツプ / SOM / 生物系統推定 / タンパク質機能推定 / 環境ゲノム / トリペプチド頻度 |
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| Research Abstract |
The homology search of base and amino acid sequences has become a basic tool in the bioinformatics field, which is essential not only for analyzing the evolution and phylogeny of genes and proteins but also for estimating the function of each protein gene in sequenced genomes. While sequence homology search is obviously useful, this method cannot estimate protein functions for almost half of genes in newly sequenced genomes, especially of novel species. To complement the sequence homology search, it is urgently required to establish methods for estimating protein functions based on different principles. By applying the BLSOM (Batch-learning SOM) method to amino-acid sequences of proteins, we established a function estimation method that utilizes clustering based on the similarity of oligopeptides frequencies. The BL-SOM for oligonucleotide frequencies could recognize genome-specific characteristics of oligonucleotide frequencies in individual genomes, permitting classification (self-organization) of genomic fragment sequences according to species without the need for species information during the calculation. We applied the BLSOMs to phylogenetic and functional prediction of a massive amount of environmental genomic sequences obtained by metagenomic analyses.
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Report
(3 results)
Research Products
(47 results)
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[Journal Article] The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota2008
Author(s)
T., Kosaka, S., Kato, T., Shimoyama, S., Ishii, T., Abe and K., Watanabe
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Journal Title
Genome Res. 18
Pages: 442-448
Description
「研究成果報告書概要(和文)」より
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Peer Reviewed
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[Journal Article] The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota2008
Author(s)
Kosaka, T., Kato, S., Shimoyama, T., Ishii, S., Abe, T., Watanabe. K.
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Journal Title
Genome Res. 18
Pages: 442-448
Description
「研究成果報告書概要(欧文)」より
Related Report
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[Journal Article] Self-Organizing Maps-its development and application2007
Author(s)
Abe, T., Ikemura, T., Kinouchi, M., Nakamura, Y., Maeno, H., Kanaya, S.
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Journal Title
Springer Japan
Pages: 12-12
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Research Signpost, Chromatin and Gene Expression2006
Author(s)
Abe, T., Sugawara, H., Kanaya, S., Kosaka, Y., Ikemura, T.
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Journal Title
DNA Structure
Pages: 16-16
Description
「研究成果報告書概要(欧文)」より
Related Report
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[Journal Article] Sequences from almost all prokaryotic, eukaryotic, and viral genomes available could be classified according to genomes on a large-scale Self-Organizing Map constructed with the Earth Simulator,2006
Author(s)
Abe, T., Sugawara, H., Kanaya, S., Ikemura, T.
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Journal Title
Journal of the Earth Simulator 6
Pages: 17-23
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[Presentation] Establishment of the Database for Genes Contributing to Sustainable World as an activity of undergraduate education.2007
Author(s)
Uehara, H., Abe, T., Tanahashi, K., Nakahara, T., Ohshima, K., Ikemura, T.
Organizer
The Genetics Society of Japan 79th Annual Meeting
Place of Presentation
Okayama
Year and Date
2007-09-03
Description
「研究成果報告書概要(欧文)」より
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[Book] DNA Structure, Chromation and Gene Expression2006
Author(s)
Abe, T., Sugawara, H., Hanaya, S., Kosaka, Y., Ikemura, T.
Publisher
Rescarch Signpost
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