Accuracy of four heuristics for the full sibship reconstruction problem in the presence of genotype errors

Konovalov, Dmitry (2006) Accuracy of four heuristics for the full sibship reconstruction problem in the presence of genotype errors. In: Proceedings of the 4th Asia-Pacific Bioinformatics Conference, pp. 7-16. From: 4th Asia-Pacific Bioninformatics Conference, 13-16 February 2006, Taipei, Taiwan.

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Abstract

The full sibship reconstruction (FSR) problem is the problem of inferring all groups of full siblings from a given population sample using genetic marker data without parental information. The FSR problem remains a significant challenge for computational biology, since an exact solution for the problem has not been found. The new algorithm, named SIMPSON-assisted Descending Ratio (SDR), is devised combining a new Simpson index based O(n2) algorithm (MS2) and the existing Descending Ratio (DR) algorithm. The SDR algorithm outperforms the SIMPSON, MS2, and DR algorithms in accuracy and robustness when tested on a variety of sample family structures. The accuracy error is measured as the percentage of incorrectly assigned individuals. The robustness of the FSR algorithms is assessed by simulating a 2% mutation rate per locus (a 1% rate per allele).

Item ID: 4321
Item Type: Conference Item (Refereed Research Paper - E1)
Keywords: population genetics; computational ecology; pedigree reconstruction
ISBN: 978-1-86094-623-3
Date Deposited: 30 Nov 2009 01:41
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960808 Marine Flora, Fauna and Biodiversity @ 100%
Citation Count from Web of Science Web of Science 2
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