Integration of plant strain SNPs using NGS Sequence Read Archive and diversity statistics analysis

2014 Fiscal Year Final Research Report

• Project/Area Number: 24500366
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: National Institute of Genetics
• Principal Investigator: KAMINUMA Eli 国立遺伝学研究所, 生命情報研究センター, 助教 (90314559)
• Co-Investigator(Renkei-kenkyūsha): NAGASAKI Hideki 国立遺伝学研究所, 生命情報研究センター, 特任研究員 (70624451) ; MOCHIZUKI Takako 情報・システム研究機構, 新領域融合研究センター, 特任研究員 (40709284)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Keywords: SNP / 次世代シークエンサ / Sequence Read Archive / 多様性指標 / データベース / 解析ワークフロー / 一塩基多型 / WGS

Outline of Final Research Achievements

In this study, an integrated database of Single Nucleotide Polymorphisms of plant strains from Sequence Read Archive was constructed as DNA Polymorphism Annotation Database(DNAPod). The integrated database is accessible from DNAPod website(http://tga.nig.ac.jp/dnapod/). Moreover, an analytical workflow for DNAPod database was implemented as a function of DDBJ Pipeline (http://p.ddbj.nig.ac.jp/). The constructed DNAPod database can be a data resource of further genomic breeding research and genomic diversity research. The integrated SNPs of rice, sorghum and maize in DNAPod are available for experimental researchers as genetic markers such as trait mapping and diversity statistics analysis.

Free Research Field

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