On the complexity of deriving position specific score matrices from positive and negative sequences

Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott

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1 Citation (Scopus)


Position-specific score matrices (PSSMs) have been applied to various problems in computational molecular biology. In this paper, we study the following problem: given positive examples (sequences) and negative examples (sequences), find a PSSM which correctly discriminates between positive and negative examples. We prove that this problem is solved in polynomial time if the size of a PSSM is bounded by a constant. On the other hand, we prove that this problem is NP-hard if the size is not bounded. We also prove hardness results for deriving multiple PSSMs and related problems.

Original languageEnglish
Pages (from-to)676-685
Number of pages10
JournalDiscrete Applied Mathematics
Issue number6-7
Publication statusPublished - Apr 1 2007
Externally publishedYes


All Science Journal Classification (ASJC) codes

  • Discrete Mathematics and Combinatorics
  • Applied Mathematics

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