Infrequent, unexpected, and contrast pattern discovery from bacterial genomes by genome-wide comparative analysis

研究成果: Chapter in Book/Report/Conference proceedingConference contribution

1 被引用数 (Scopus)

抄録

With plenty of sequences, comparative genomics is becoming important. Its basic approach is to find similar subsequences from the sequences of different species and then examine differences in detail among found similar parts. Instead of focusing on similar parts, this paper is devoted to find different parts directly from the whole DNA sequences. It is challenging because the large size prohibits computationally expensive methods and there exits so many differences in case of genome-wide comparison. To cope with this, we exploit the algorithm in (Ikeda and Suzuki, 2009), which finds unexpected, infrequent patterns. But, found patterns was not evaluated from the viewpoint of biology. In this paper, we show that patterns discovered by the algorithm from bacterial genome sequences match well biological features, such as RNA and transposon. Therefore, assuming these features as relevant regions, we compute F-measure values and show that some species achieves about 90%, which is one order of magnitude better than patterns found by an existing method. Thus, we conclude that the algorithm can find these infrequent, but biologically meaningful patterns from genome-wide sequences.

本文言語英語
ホスト出版物のタイトルBIOINFORMATICS 2013 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms
ページ308-311
ページ数4
出版ステータス出版済み - 5 27 2013
イベントInternational Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2013 - Barcelona, スペイン
継続期間: 2 11 20132 14 2013

その他

その他International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2013
国/地域スペイン
CityBarcelona
Period2/11/132/14/13

All Science Journal Classification (ASJC) codes

  • 生体医工学
  • 健康情報学
  • モデリングとシミュレーション

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