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  1. 学術雑誌論文
  2. その他
  1. 部局別インデックス
  2. 工学部

Rule-based Assembly for Short-read Datasets Obtained with Multiple Assemblers and k-mer Sizes

http://hdl.handle.net/20.500.12000/47510
http://hdl.handle.net/20.500.12000/47510
19edfbd9-d57c-45ad-8d59-2bc20ef4b623
名前 / ファイル ライセンス アクション
10_9.pdf 10_9.pdf
Item type デフォルトアイテムタイプ(フル)(1)
公開日 2020-12-16
タイトル
タイトル Rule-based Assembly for Short-read Datasets Obtained with Multiple Assemblers and k-mer Sizes
言語 en
作成者 Ohshiro, Ayako

× Ohshiro, Ayako

en Ohshiro, Ayako

Afuso, Hitoshi

× Afuso, Hitoshi

en Afuso, Hitoshi

Okazaki, Takeo

× Okazaki, Takeo

en Okazaki, Takeo

Nakamura, Morikazu

× Nakamura, Morikazu

en Nakamura, Morikazu

アクセス権
アクセス権 open access
アクセス権URI http://purl.org/coar/access_right/c_abf2
権利情報
言語 ja
権利情報 © 2017 by the Information Processing Society of Japan
主題
言語 en
主題Scheme Other
主題 DNA assembly
言語 en
主題Scheme Other
主題 k-mer
言語 en
主題Scheme Other
主題 hybrid assembly
言語 en
主題Scheme Other
主題 decision tree
言語 en
主題Scheme Other
主題 C4.5
内容記述
内容記述タイプ Other
内容記述 Various de novo assembly methods based on the concept of k-mer have been proposed. Despite the success of these methods, an alternative approach, referred to as the hybrid approach, has recently been proposed that combines different traditional methods to effectively exploit each of their properties in an integrated manner. However, the results obtained from the traditional methods used in the hybrid approach depend not only on the specific algorithm or heuristics but also on the selection of a user-specific k-mer size. Consequently, the results obtained with the hybrid approach also depend on these factors. Here, we designed a new assembly approach, referred to as the rule-based assembly. This approach follows a similar strategy to the hybrid approach, but employs specific rules learned from certain characteristics of draft contigs to remove any erroneous contigs and then merges them. To construct the most effective rules for this purpose, a learning method based on decision trees, i.e., a complex decision tree, is proposed. Comparative experiments were also conducted to validate the method. The results showed that proposed method could outperformed traditional methods in certain cases.
内容記述タイプ Other
内容記述 論文
出版者
言語 ja
出版者 情報処理学会
言語
言語 eng
資源タイプ
資源タイプ journal article
資源タイプ識別子 http://purl.org/coar/resource_type/c_6501
出版タイプ
出版タイプ VoR
出版タイプResource http://purl.org/coar/version/c_970fb48d4fbd8a85
識別子
識別子 http://hdl.handle.net/20.500.12000/47510
識別子タイプ HDL
関連情報
関連識別子
識別子タイプ DOI
関連識別子 https://doi.org/10.2197/ipsjtbio.10.9
関連識別子
識別子タイプ DOI
関連識別子 https://doi.org/10.2197/ipsjtbio.10.9
収録物識別子
収録物識別子タイプ ISSN
収録物識別子 1882-6679
収録物名
言語 en
収録物名 IPSJ Transactions on Bioinformatics
書誌情報
巻 10, p. 9-15
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