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Bioinformatics Vol. 16 no. 10 2000
Pages 923-931
© 2000 Oxford University Press

Original Paper

The reduction of large molecular profiles to informative components using a Genetic Algorithm

F. M. Stefanini 1, and A. Camussi 2

1 Department of Statistics ‘G.Parenti’, University of Florence, Viale Morgagni 59, 50134, Firenze, Italy
2 Department of Agricultural Biotechnology, University of Florence, P.le delle Cascine, 24, 50144, Firenze, Italy

Received on August 17, 1999 ; accepted on May 10, 2000

Motivation: Molecular profiles (DNA fingerprints) may be used to allocate an individual of unknown membership to one among the known groups of a reference population. Time and costs of profile assessment may be reduced by identifying informative profile components (markers).

Results: A genetic algorithm (GA) is proposed to identify promising candidate markers from a pilot experiment in which observations are supposed to be without measurement error. The analysis of simulated datasets suggests reasonable values for GA parameters and confirms that the GA finds components of the profile showing association with the considered groups. Our GA may be used to perform a first screening of candidate markers to be included in subsequent experiments.

Availability: The 32-bit executable (Windows 95, 98 and NT) is available at http://www.ds.unifi.it/~stefanin/bioinformatics.htm.

Contact: stefanin@ds.unifi.it

Supplementary Information: The algorithm is implemented for research purposes, i.e. a limited amount of input filtering and error messages are provided.

To whom correspondence should be addressed.


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