2007 Fiscal Year Final Research Report Summary
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)
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| Project Period (FY) |
2006 – 2007
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| Keywords | Bioinformatics / Environmental microorganisms / SOM / Protein function prediction / Phylogenetic prediction / Self-Organizing Map / Earth Simulator / Methagenome |
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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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[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
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
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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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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
Description
「研究成果報告書概要(欧文)」より
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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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