Extracting best consensus motifs from positive and negative examples

Erika Tateishi, Osamu Maruyama, Satoru Miyano

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

3 被引用数 (Scopus)

抄録

We define the best consensus motif (BCM) problem motivated by the problem of extracting motifs from nucleic acid and amino acid sequences. A type over an alphabet Σ is a family Ω of subsets of Σ *. A motif π of type Ω is a string π=π1 ... πn of motif components, each of which stands for an element in Ω. The BCM problem for Ω is, given a yes-no sample S={(α (1)(1),..., (α(m)(m))} of pairs of strings in Σ* with α (i) ≠β(i) for 1 ≤ i ≤ m, to find a motif π of type Ω that maximizes the number of good pairs in S, where (α (i), β (i)) is good for π if π accepts α (i) and rejects β (i) We prove that the BCM problem is NP-complete even for a very simple type (Formula presented), which is used, in practice, for describing protein motifs in the PROSITE database. We also show that the NP-completeness of the problem does not change for the type Ω 1∪ {Σ+}∪{Σ[i,j]1≤i≤ j}, where Σ [i,j] is the set of strings over Σ of length between i and j Furthermore, for the BCM problem for Ω 1 we provide a polynomial-time greedy algorithm based on the probabilistic method. Its performance analysis shows an explicit approximation ratio of the algorithm.

本文言語英語
ホスト出版物のタイトルSTACS 1996 - 13th Annual Symposium on Theoretical Aspects of Computer Science, Proceedings
編集者Claude Puech, Rudiger Reischuk
出版社Springer Verlag
ページ219-230
ページ数12
ISBN(印刷版)9783540609223
DOI
出版ステータス出版済み - 1996
イベント13th Annual Symposium on Theoretical Aspects of Computer Science, STACS 1996 - Grenoble, フランス
継続期間: 2 22 19962 24 1996

出版物シリーズ

名前Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
1046
ISSN(印刷版)0302-9743
ISSN(電子版)1611-3349

その他

その他13th Annual Symposium on Theoretical Aspects of Computer Science, STACS 1996
国/地域フランス
CityGrenoble
Period2/22/962/24/96

All Science Journal Classification (ASJC) codes

  • 理論的コンピュータサイエンス
  • コンピュータ サイエンス(全般)

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