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

N1 - Funding Information:
Partially supported by a Grant-in-Aid “Genome Information Science” and a Grant-in-Aid No. 16300092 from The Ministry of Education, Science, Sports and Culture in Japan. A preliminary version of this paper appeared in the Proceedings of CPM 2002, Springer, Lecture Notes in Computer Science, vol. 2373, 2002.

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.

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U2 - 10.1016/j.dam.2004.10.011

DO - 10.1016/j.dam.2004.10.011

M3 - Article

AN - SCOPUS:33846889735

VL - 155

SP - 676

EP - 685

JO - Discrete Applied Mathematics

JF - Discrete Applied Mathematics

SN - 0166-218X

IS - 6-7

ER -