An application of nonlinear optimization in molecular biology

A maximum likelihood approach has been proposed for finding protein binding sites on strands of DNA [G.D. Stormo, G.W. Hartzell, Proceedings of the National Academy of Sciences of the USA 86 (1989) 1183]. We formulate an optimization model for the problem and present calculations with experimental s...

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Bibliographic Details
Published in:European journal of operational research 2002-04, Vol.138 (2), p.452-458
Main Authors: Ecker, J.G, Kupferschmid, M, Lawrence, C.E, Reilly, A.A, Scott, A.C.H
Format: Article
Language:English
Subjects:
Algorithms
Binding sites
DNA sequences
Maximum likelihood
Maximum likelihood estimation
Molecular biology
Nonlinear programming
Optimization
Protein binding
Proteins
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Summary:A maximum likelihood approach has been proposed for finding protein binding sites on strands of DNA [G.D. Stormo, G.W. Hartzell, Proceedings of the National Academy of Sciences of the USA 86 (1989) 1183]. We formulate an optimization model for the problem and present calculations with experimental sequence data to study the behavior of this site identification method.
ISSN:0377-2217
1872-6860
DOI:10.1016/S0377-2217(01)00122-9