Ranked solutions to a class of combinatorial optimizations - With applications in mass spectrometry based peptide sequencing and a variant of directed paths in random media

Physica A: Statistical Mechanics and its Applications

Volumn 354, Issue 1-4, 2005, Pages 558-570

  Doerr, Timothy P ^a   Alves, Gelio ^a   Yu, Yi Kuo ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Combinatorial optimization; Directed paths in random media; Dynamic programming; Statistical significance

Indexed keywords

FUNCTIONS; ITERATIVE METHODS; MASS SPECTROMETRY; MATHEMATICAL TRANSFORMATIONS; OPTIMIZATION; POLYNOMIALS; STATISTICAL METHODS;

COMBINATORIAL OPTIMIZATIONS; RANDOM MEDIA; RANDOM MEDIA PROBLEM; TRANSFER MATRIX;

COMBINATORIAL MATHEMATICS;

EID: 19944405087     PISSN: 03784371     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.physa.2005.03.004     Document Type: Article

References (6)

1. M.R. Garey, and D.S. Johnson Computers and Intractability 1979 W.H. Freeman and Company New York
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3. M. Kardar Nucl. Phys. B 290 1987 582
4. D.S. Fisher, and D.A. Huse Phys. Rev. B 43 1991 10728
5. G. Alves, Yi-Kuo Yu, Robust Accurate Identification of Peptides (RAId): Deciphering MS 2 Data Using a Structured Library Search with de novo Based Statistics, Proc. Natl. Acad. Sci. USA, manuscript in preparation.
6. A previous article did use a somewhat similar method to obtain a parameter characterizing sequence alignments. See Maik Kschischo, Michael Lässig, and Yi-Kuo Yu, Bulletin of Mathematical Biology 67 (2005) 169. While the previous case used scaling and an iterative map to generate solutions in a certain region of parameter space from a pair of classes of exact solutions, the current method uses no exact solutions, only the approximate rankings.