### Abstract

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 language | English |
---|---|

Pages (from-to) | 676-685 |

Number of pages | 10 |

Journal | Discrete Applied Mathematics |

Volume | 155 |

Issue number | 6-7 |

DOIs | |

Publication status | Published - Apr 1 2007 |

Externally published | Yes |

### Fingerprint

### All Science Journal Classification (ASJC) codes

- Discrete Mathematics and Combinatorics
- Applied Mathematics

### Cite this

*Discrete Applied Mathematics*,

*155*(6-7), 676-685. https://doi.org/10.1016/j.dam.2004.10.011

**On the complexity of deriving position specific score matrices from positive and negative sequences.** / Akutsu, Tatsuya; Bannai, Hideo; Miyano, Satoru; Ott, Sascha.

Research output: Contribution to journal › Article

*Discrete Applied Mathematics*, vol. 155, no. 6-7, pp. 676-685. https://doi.org/10.1016/j.dam.2004.10.011

}

TY - JOUR

T1 - On the complexity of deriving position specific score matrices from positive and negative sequences

AU - Akutsu, Tatsuya

AU - Bannai, Hideo

AU - Miyano, Satoru

AU - Ott, Sascha

PY - 2007/4/1

Y1 - 2007/4/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=33846889735&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33846889735&partnerID=8YFLogxK

U2 - 10.1016/j.dam.2004.10.011

DO - 10.1016/j.dam.2004.10.011

M3 - Article

VL - 155

SP - 676

EP - 685

JO - Discrete Applied Mathematics

JF - Discrete Applied Mathematics

SN - 0166-218X

IS - 6-7

ER -