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2011 Fiscal Year Final Research Report

Developing fast algorithm for analyzing Giga-sequence data

Research Project

  • PDF
Project/Area Number 22700319
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Bioinformatics/Life informatics
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

SHIMIZU Kana  独立行政法人産業技術総合研究所, 生命情報工学研究センター, 研究員 (60367050)

Project Period (FY) 2010 – 2011
Keywordsゲノム / ギガシークエンサー / アルゴリズム
Research Abstract

Next Generation Sequencing(NGS) technology calls for fast and accurate algorithms that can evaluate sequence similarity for a huge amount data. In this study, we designed and implemented exact algorithm SlideSort that finds all similar pairs whose edit-distance does not exceed a given threshold from NGS data, which helps many important analyses, such as de novo genome assembly, identification of frequently appearing sequence patterns and accurate clustering. In comparison to state-of-the-art methods, our method is much faster in finding remote matches, scaling easily to tens of millions of sequences. Our software has an additional function of single link clustering, which is useful in summarizing NGS data for further processing.

  • Research Products

    (7 results)

All 2011 2010 Other

All Journal Article (1 results) (of which Peer Reviewed: 1 results) Presentation (4 results) Remarks (1 results) Patent(Industrial Property Rights) (1 results)

  • [Journal Article] All Pairs Similarity Search for Short Reads2011

    • Author(s)
      Kana Shimizu, Koji Tsuda, SlideSort
    • Journal Title

      Bioinformatics

      Volume: 27(4) Pages: 464-470

    • DOI

      DOI:10.1093/bioinformatics/btq677

    • Peer Reviewed
  • [Presentation] Fast and exact algorithm for Next Generation Sequencing data analysis2011

    • Author(s)
      Kana Shimizu, Koji Tsuda
    • Organizer
      ISMB/ECCB 2011 Highlights Track
    • Place of Presentation
      Vienna
    • Year and Date
      2011-07-18
  • [Presentation] SlideSort : A fast and exact tool for finding all similar pairs from next-generation sequencing data2011

    • Author(s)
      Kana Shimizu, Koji Tsuda
    • Organizer
      RECOMB 2011
    • Place of Presentation
      Vancouver
    • Year and Date
      2011-03-29
  • [Presentation] SLIDESORT : All pairs similarity search for short reads2010

    • Author(s)
      Kana Shimizu, Koji Tsuda
    • Organizer
      2010年日本バイオインフォマティクス学会年会
    • Place of Presentation
      九州
    • Year and Date
      2010-12-15
  • [Presentation] Developing an exact method to find similar pairs with small edit-distance2010

    • Author(s)
      Kana Shimizu, Koji Tsuda
    • Organizer
      ISMB 2010
    • Place of Presentation
      Boston
    • Year and Date
      2010-07-12
  • [Remarks]

    • URL

      http://www.cbrc.jp/~shimizu/slidesort/index.php

  • [Patent(Industrial Property Rights)] 配列解析装置,配列解析方法およびコンピュータプログラム2010

    • Inventor(s)
      清水佳奈,津田宏治
    • Industrial Property Rights Holder
      産業技術総合研究所
    • Industrial Property Number
      特許、2010-156342
    • Filing Date
      2010-07-09

URL: 

Published: 2013-07-31  

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