Abstract
PSSMs (Position-Specific Score Matrices) have been applied to various problems in Bioinformatics. 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 similar results on deriving a mixture of PSSMs.
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References
Akutsu, T., Yagiura, M.: On the complexity of deriving score functions from examples for problems in molecular biology. Proc. ICALP’98. Lecture Notes in Computer Science, Vol. 1443. Springer-Verlag, Berlin Heidelberg New York (1998) 832–843
Akutsu, T., Arimura, H., Shimozono, S.: On approximation algorithms for local multiple alignment. Proc. 4th ACM Int. Conf. Computational Molecular Biology (2000) 1–7
Durbin, R., Eddy, S., Krogh, A., Mitchison, G.: Biological Sequence Analysis. Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press (1998)
Edelsbrunner, H.: Algorithms in Combinatorial Geometry. Springer-Verlag, Berlin Heidelberg New York (1987)
Garey, M. R., Johnson, D. S.: Computers and Intractability. Freeman (1979)
Henikoff, S., Henikoff, J. G.: Amino acid substitution matrices from protein blocks. Proc. National Academy of Sciences of the USA 89 (1992) 10915–10919
Jiang, T., Li, M.: On the complexity of learning strings and sequences. Proc. 4th ACM Workshop on Computational Learning Theory (1991) 367–274
Kann, M., Qian, B., Goldstein, R. A.: Optimization of a new score function for detection of remote homologs. Proteins 41 (2000) 498–503
Kyte, J., Doolittle, R. F.: A simple method for displaying the hydropathic character of a protein. J. Molecular Biology 157 (1982) 105–132
Lanctot, K., Li, M., Ma, B., Wang, S., Zhang, L.: Distinguishing string selection problems. Proc. 10th ACM-SIAM Symp. Discrete Algorithms (1999) 633–642
Li, M., Ma, B., Wang, L.: Finding similar regions in many strings. Proc. 31st ACM Symp. Theory of Computing (1999) 473–482
Miyano, S., Shinohara, A., Shinohara, T.: Which classes of elementary formal systems are polynomial-time learnable. Proc. 2nd Workshop on Algorithmic Learning Theory (1991) 139–150
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Akutsu, T., Bannai, H., Miyano, S., Ott, S. (2002). On the Complexity of Deriving Position Specific Score Matrices from Examples. In: Apostolico, A., Takeda, M. (eds) Combinatorial Pattern Matching. CPM 2002. Lecture Notes in Computer Science, vol 2373. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45452-7_15
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DOI: https://doi.org/10.1007/3-540-45452-7_15
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