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Development of novel RNA-seq and assemble method for gene structure annotation

Research Project

Project/Area Number 16K14641
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Genome biology
Research InstitutionTokyo Institute of Technology

Principal Investigator

ITOH Takehiko  東京工業大学, 生命理工学院, 教授 (90501106)

Project Period (FY) 2016-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2017: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2016: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
Keywords遺伝子構造予測 / RNA-seq / 遺伝子予測 / 遺伝子配列構築
Outline of Final Research Achievements

In this research program, we have constructed a novel gene structure annotation protocol using both experimental and computational analyses. In the experimental analysis, the 5′ end of cDNA was protected. Then, the digestion reaction from the 3′ end was performed using Exo3. Finally, from the 5′ end, one sample was obtained, while from the 3′ end various samples were obtained. Next, we constructed an Illumina library from these samples, but we were not successful in the preparation of samples ranging from around 1,000 bp, even using various protocols. In the computational analysis, we succeeded in constructing a novel cDNA assembly program for the abovementioned data, and the performance of the simulation data was satisfactory. We did not succeed in achieving the initial target, but we could obtain 5′ and 3′ end contigs from the same cDNA; this information is very useful for gene identification. Hence, this program can be applied to improve the accuracy of gene identification.

Report

(3 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • Research Products

    (1 results)

All 2017

All Presentation (1 results)

  • [Presentation] Platanus2: a de novo haplotype assembler enabling comprehensive accesses to divergent heterozygous region.2017

    • Author(s)
      梶谷嶺,吉村大,奥野未来,豊田敦,伊藤武彦
    • Organizer
      第6回生命医薬情報学連合大会(IIBMP2017)
    • Related Report
      2017 Annual Research Report

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Published: 2016-04-21   Modified: 2019-03-29  

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