Method for search based character optimization

Details Method for search based character optimization Method for search based character optimization

2006-05-09

2006-05-09

Martinell, James (Department: 1634)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Biological or biochemical

C702S020000

Reexamination Certificate

active

07043371

ABSTRACT:
A method for selecting a sequence is provided. A set of sequences are defined, each one of the sequences comprising one or more characters. A sub-set of the set of sequences are evaluated with a dynamic programing method to obtain a numeric indicia of merit. Additional sequences are added into the sub-set of sequences. The steps of defining, evaluating, and adding are repeated until the numeric indicia is substantially constant or there are no more additional sequences. One or more of the sequences are selected based on the numeric indicia.

REFERENCES:
Mount, D.W., Bioinformatics—Sequence and Genome Analysis, Mar. 15, 2001, Mount, Cold Spring Harbor Laboratory Press, pp. 19-137.
Ward Wheeler, “Alignment characters, dynamic programming and heuristic solutions”, R. DeSalle, B. Schierwater (eds) Molecular Approaches to Ecology and Evolution (1998), pp. 243-251.
Ward Wheeler, “Fixed Character States and the Optimization of Molecular Sequence Data”, 15 Cladistics; 379-385 (1999).
Ward Wheeler, “Homology and the Optimization of DNA Sequence Data”, 17 Cladstics; S3-S11 (2001).
Aloysius Phillips, Daniel Janies, and Ward Wheeler, “Multiple Sequence Alignment in Phylogenetic Analysis”, 16 Mol. Phyl. and Evol., 317-330 (2000).
Ward Wheeler, “Optimization Alignment: The End of Multiple Sequence Alignment in Phylogenetics?”, 12 Cladistics, 1-9 (1996).
Daniel Janies and Ward Wheeler, “Poy Documentation Binaries Update Nov. 30, 2000”, (2000).
Wheeler, et al., “The Phylogeny of the Extant Hexapod Orders”, 17 Cladistics, 113-169 (2001).

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