A bioinformatics strategy to clarify microbial community structures by analyzing metagenomic sequences on the basis of Batch-Learning Self-Organizing Map
| Project/Area Number |
20700273
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| Research Category |
Grant-in-Aid for Young Scientists (B)
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| Allocation Type | Single-year Grants |
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| Research Field |
Bioinformatics/Life informatics
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| Research Institution | Nagahama Institute of Bio-Science and Technology |
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Principal Investigator |
ABE Takashi Nagahama Institute of Bio-Science and Technology, バイオサイエンス学部, 助教 (30390628)
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| Project Period (FY) |
2008 – 2010
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| Project Status |
Completed (Fiscal Year 2010)
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| Budget Amount *help |
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2010: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2009: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2008: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
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| Keywords | メタゲノム / 塩基組成 / 環境微生物 / 系統推定 / 自己組織化マップ / 連続塩基組成 / 連続塩基頻度 |
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| Research Abstract |
Metagenomic approach, which is the genome analysis on a mixture of uncultured microorganisms, has been recently developed to search for novel and industrially useful genes and to study microbial diversity in a wide variety of environments. We have previously developed a Batch-Learning SOM (BLSOM) for genome informatics, which does not depend on the order of data input. Here we used BLSOM as a novel bioinformatics strategy to unveil and visualize microbial community structures and relative abundance of microorganisms within an environmental sample. The present method is also useful for surveys of microorganisms in extremity environment samples and novel pathogenetic microorganisms in clinical samples.
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Report
(4 results)
Research Products
(107 results)
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[Journal Article] tRNADB-CE 2011 : tRNA gene database curated manually by experts.2011
Author(s)
Takashi Abe, Toshimichi Ikemura, Junichi Sugahara, Akio Kanai, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi
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Journal Title
Nucleic Acids Research 39
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[Journal Article] tRNADB-CE 2011 : tRNA gene database curated manually by experts.2011
Author(s)
T.Abe, T.Ikemura, J.Sugahara, A.Kanai, Y.Ohara, H.Uehara, M.Kinouchi, S.Kanaya, Y.Yamada, A.Muto, H.Inokuchi.
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Journal Title
Nucleic Acids Research
Volume: 39
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Peer Reviewed
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[Presentation] tRNADB-CE : Trna gene database curated manually by experts.2010
Author(s)
Takashi Abe, Toshimichi Ikemura, yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Junichi Sugahara, Akio Kanai, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi
Organizer
23rd Trna workshop
Place of Presentation
Aveiro, Portugal(oral)
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[Presentation] tRNADB-CE : tRNA gene database curated manually by experts2010
Author(s)
阿部貴志, 池村淑道, 小原康雄, 上原啓史, 木ノ内誠, 菅原潤一, 金井明夫, 金谷重彦, 山田優子, 井口八郎
Organizer
23rd tRNA workshop, (oral)
Place of Presentation
Aveiro, Portugal
Related Report
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[Presentation] tRNADB-CE:エキスパートがキュレートしたtRNA遺伝子データベース2009
Author(s)
阿部貴志, 池村淑道, 小原康雄, 上原啓史, 平野晋也, 木ノ内誠, 金谷重彦, 菅原潤一, 金井明夫, 山田優子, 武藤〓, 井口八郎
Organizer
第32回日本分子生物学会年会(ポスタ)
Place of Presentation
パシフィコ横浜(横浜)
Year and Date
2009-12-11
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[Presentation] tRNADB-CE:エキスパートがキーユレートしたtRNA遺伝子データベース2009
Author(s)
阿部貴志, 池村淑道, 小原康雄, 上原啓史, 平野晋也, 木ノ内誠, 金谷重彦, 菅原潤一, 金井明夫, 山田優子, 武藤〓, 井口八郎
Organizer
RNA学会第11回大会
Place of Presentation
新潟(口頭)
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[Presentation] Diversity of green-like ribulose-1,5-bisphosphate carboxylase/oxygenase(RuBisCO)Large-subunit genes in an Antarctic moss pillar2009
Author(s)
R.Nakai, T.Abe, T.Baba, S.Imura, H.Kagoshima, H.Kanda, Y.Kohara, T.Naganuma, H.Niki, K.Yanagihara
Organizer
Xth SCAR International Biology Symposium, (Oral)
Place of Presentation
Hokkaido Univ., Sapporo
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[Presentation] tRNADB-CE:エキスパートがキュレートしたtRNA遺伝子データベース2009
Author(s)
阿部貴志, 池村淑道, 小原康雄, 上原啓史, 平野晋也, 木ノ内誠, 金谷重彦, 菅原潤一, 金井明夫, 山田優子, 武藤〓, 井口八郎
Organizer
RNA学会第11回大会(Oral)
Place of Presentation
朱鷺メッセ(新潟)
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