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
SN - 0166-218X
VL - 155
SP - 676
EP - 685
JO - Discrete Applied Mathematics
JF - Discrete Applied Mathematics
IS - 6-7
ER -