A bioinformatics strategy for revealing microbial community structures and metabolic pathways by reconstructing multiple genomes from metagenomic sequences.
| Project/Area Number |
23710242
|
|---|
| Research Category |
Grant-in-Aid for Young Scientists (B)
|
| Allocation Type | Multi-year Fund |
|---|
| Research Field |
Applied genomics
|
|---|
| Research Institution | Niigata University |
|---|
Principal Investigator |
ABE Takashi 新潟大学, 自然科学系, 准教授 (30390628)
|
|---|
| Project Period (FY) |
2011 – 2013
|
| Project Status |
Completed (Fiscal Year 2013)
|
| Budget Amount *help |
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2013: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2011: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
|
|---|
| Keywords | メタゲノム / 一括学習型自己組織化マップ / 連続塩基 / 連続アミノ酸 / 生物系統推定 / タンパク質機能推定 / ランダム配列 / 連続塩基組成 |
|---|
| Research Abstract |
Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes useful in medical and industrial applications. BLSOM is the most suitable for phylogenetic assignment of metagenomic sequences because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition.
We constructed oligonucleotide-BLSOMs for all available sequences from species-known genomes, and by mapping metagenomic sequences on this large-scale BLSOMs, we could predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms including viruses. This software will be freely available at our website. We also developed another BLSOM strategy for clustering metagenomic sequences according to genome, and for function prediction of poorly-characterized protein genes obtained from metagenome analysis.
|
Report
(4 results)
Research Products
(65 results)
-
-
-
-
-
-
-
-
-
-
-
-
[Journal Article] Systematization of diversity of protein sequences in enzymes related to secondary metabolic pathways in plants in the context of big data biology inspired by KNApSAcK Motorcycle database.2013
Author(s)
Shun Ikeda*, Takashi Abe*, Yukiko Nakamura, Kibinge Nelson, Aki Hirai Morita, Atsushi Nakatani, Naoaki Ono, Toshimichi Ikemura, Kensuke Nakamura, Md. Altaf-Ul-Amin, Shigehiko Kanaya (*equal contribution).
-
Journal Title
Plant and Cell Physiology
Volume: 54
Pages: 711-727
Related Report
Peer Reviewed
-
-
[Journal Article] Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics2013
Author(s)
Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T, Yamada Y, Muto A, Inokuchi H, Ikemura T, Matsumoto T, Sasaki T, Itoh T.
-
Journal Title
Plant Cell Physiol.
Volume: 52
Issue: 2
Pages: e6-e6
DOI
Related Report
Peer Reviewed
-
-
-
-
-
-
[Journal Article] Microflorae of aquatic moss pillars in a freshwater lake, East Antarctica, based on fatty acid and 16S rRNA gene analyses2012
Author(s)
Ryosuke Nakai, Takashi Abe, Tomoya Baba, Satoshi Imura, Hiroshi Kagoshima, Hiroshi Kanda, Atsuko Kanekiyo, Yuji Kohara, Akiko Koi, Keiko Nakamura, Takanori Narita, Hironori Niki, Katsuhiko Yanagihara, Takeshi Naganuma
-
Journal Title
Polar Biology
Volume: 35
Issue: 3
Pages: 425-433
DOI
Related Report
Peer Reviewed
-
[Journal Article] Eukaryotic phylotypes in aquatic moss pillars inhabiting a freshwater lake in East Antarctica, based on 18S rRNA gene analysis.2012
Author(s)
Nakai R, Abe T, Baba T, Imura S, Kagoshima H, Kanda H, Kohara Y, Koi A, Niki H, Yanagihara K, Naganuma T
-
Journal Title
Polar Biology
Volume: 35
Issue: 10
Pages: 1495-1504
DOI
Related Report
Peer Reviewed
-
[Journal Article] Diversity of RuBisCO gene responsible for CO_2 fixation in an Antarcticmoss pillar.2012
Author(s)
Nakai R, Abe T, Baba T, Imura S, Kagoshima H, Kanda H, Kohara Y, Koi A, Niki H, Yanagihara K, Naganuma T
-
Journal Title
Polar Biology
Volume: 35
Issue: 11
Pages: 1641-1650
DOI
Related Report
Peer Reviewed
-
-
-
-
-
-
-
-
-
-
-
-
[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, and Hachiro Inokuchi.
-
Journal Title
Nucleic Acids Research.
Volume: 39
Related Report
Peer Reviewed
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
