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Regulatory DNA conserved between Phyla

Research Project

Project/Area Number 26700030
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypePartial Multi-year Fund
Research Field Life / Health / Medical informatics
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

Frith Martin  国立研究開発法人産業技術総合研究所, 情報・人間工学領域, 上級主任研究員 (40462832)

Project Period (FY) 2014-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥18,850,000 (Direct Cost: ¥14,500,000、Indirect Cost: ¥4,350,000)
Fiscal Year 2016: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2015: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Fiscal Year 2014: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Keywordsgenome / orthology / alignment / probability / substitution / insertion / deletion / バイオインフォマティクス / 生体情報学 / 比較ゲノム
Outline of Final Research Achievements

This year, several direct and indirect research outcomes were finalized and published. A survey of sequence rearrangements in human DNA was published in NAR. A simplified "child table" algorithm, for finding similar sequences, was published in IEEE/ACM TCBB. A method for detecting genome variations was published in BMC Medical Genomics. Our method for considering DNA neighbor-base preferences, which improves bacterial strain discrimination, was published in BMC Bioinformatics. Our analysis methods are proving useful for recent "long" DNA-read data.

Report

(5 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (15 results)

All 2018 2017 2016 2015 Other

All Journal Article (7 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 7 results,  Open Access: 7 results,  Acknowledgement Compliant: 3 results) Presentation (7 results) (of which Int'l Joint Research: 1 results) Remarks (1 results)

  • [Journal Article] A Simplified Description of Child Tables for Sequence Similarity Search2018

    • Author(s)
      Frith Martin、Shrestha Anish
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: - Issue: 6 Pages: 1-1

    • DOI

      10.1109/tcbb.2018.2796064

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A survey of localized sequence rearrangements in human DNA2017

    • Author(s)
      Frith Martin C、Khan Sofia
    • Journal Title

      Nucleic Acids Research

      Volume: 46 Issue: 4 Pages: 1661-1673

    • DOI

      10.1093/nar/gkx1266

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] EAGLE: Explicit Alternative Genome Likelihood Evaluator.2017

    • Author(s)
      Tony Kuo, Martin Frith, Jun Sese, Paul Horton
    • Journal Title

      BMC Medical Genomics

      Volume: 11 Issue: Suppl 2 Pages: 28-28

    • DOI

      10.1186/s12920-018-0342-1

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads2017

    • Author(s)
      Poulsen Thomas M.、Frith Martin
    • Journal Title

      BMC Bioinformatics

      Volume: 18 Issue: 1 Pages: 299-299

    • DOI

      10.1186/s12859-017-1710-0

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Training alignment parameters for arbitrary sequencers with LAST-TRAIN2017

    • Author(s)
      Hamada M, Ono Y, Asai K, Frith MC
    • Journal Title

      Bioinformatics

      Volume: 33 Issue: 6 Pages: 926-928

    • DOI

      10.1093/bioinformatics/btw742

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] ALP & FALP: C++ libraries for pairwise local alignment E-values2016

    • Author(s)
      Sheetlin S, Park Y, Frith MC, Spouge JL
    • Journal Title

      Bioinformatics

      Volume: 32 Pages: 304-5

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Split-alignment of genomes finds orthologies more accurately2015

    • Author(s)
      MC Frith, R Kawaguchi
    • Journal Title

      Genome Biology

      Volume: 16 Issue: 1 Pages: 106-106

    • DOI

      10.1186/s13059-015-0670-9

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] Aligning sequences with arbitrary rearrangements and duplications2017

    • Author(s)
      Martin Frith, Risa Kawaguchi, Michiaki Hamada
    • Organizer
      Advanced Genome Science International Symposium
    • Place of Presentation
      University of Tokyo, Tokyo
    • Year and Date
      2017-01-10
    • Related Report
      2016 Annual Research Report
  • [Presentation] Training alignment parameters for PacBio, Ion Torrent and Nanopore sequencers with last-train2016

    • Author(s)
      Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin Frith
    • Organizer
      WABI 2016
    • Place of Presentation
      Aarhus University, Aarhus, Denmark
    • Year and Date
      2016-08-22
    • Related Report
      2016 Annual Research Report
  • [Presentation] LAST: statistically rigorous, large-scale sequence comparison2016

    • Author(s)
      Martin Frith
    • Organizer
      WABI 2016
    • Place of Presentation
      Aarhus University, Aarhus, Denmark
    • Year and Date
      2016-08-22
    • Related Report
      2016 Annual Research Report
  • [Presentation] A survey of genome rearrangements in human evolution2015

    • Author(s)
      MC Frith
    • Organizer
      29th International Mammalian Genome Conference (IMGC)
    • Place of Presentation
      Yokohama Port Memorial Hall(Yokohama, Kanagawa)
    • Year and Date
      2015-11-11
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Split-alignment of genomes finds orthologies more accurately2015

    • Author(s)
      MC Frith, R Kawaguchi
    • Organizer
      GIW/InCoB
    • Place of Presentation
      MIRAIKAN(Odaiba, Tokyo)
    • Year and Date
      2015-09-09
    • Related Report
      2015 Annual Research Report
  • [Presentation] Explaining the correlations among properties of mammal promoters2015

    • Author(s)
      MC Frith
    • Organizer
      ISCB Africa
    • Place of Presentation
      Dar es Salaam
    • Year and Date
      2015-03-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] Nanopore Sequencing for Genotyping Pathogens of Tropical Diseases2015

    • Author(s)
      T Kischka, MC Frith, N Grundman, J Jamagishi, Y Suzuki, W Makalowski
    • Organizer
      ISCB Africa
    • Place of Presentation
      Dar es Salaam
    • Year and Date
      2015-03-10
    • Related Report
      2014 Annual Research Report
  • [Remarks] local-rearrangements

    • URL

      https://github.com/mcfrith/local-rearrangements

    • Related Report
      2017 Annual Research Report

URL: 

Published: 2014-04-04   Modified: 2019-03-29  

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