Document RAIRO-Theor. Inf. Appl. 42, 323-333 (2008)
DOI: 10.1051/ita:2007034
Phenotype space and kinship assignment for the simpson index
Bruce Litow and Dmitry KonovalovBioinformatics Applications Research Centre, School of MP & IT, James Cook University, Townsville, Qld. 4811, Australia; bruce.litow@jcu.edu.au; dmitry.konovalov@jcu.edu.au
(Received October 6, 2006. Accepted August 3, 2007. Published online 6 September 2007.)
Abstract
We investigate the computational structure of the biological kinship assignment problem by abstracting away all biological details that are irrelevant to computation. The computational structure depends on phenotype space, which we formally define.
We illustrate this approach by exhibiting an approximation algorithm for
kinship assignment in the case of the Simpson index with a priori error bound and
running time that is polynomial in the bit size of the population, but exponential in phenotype space size.
This algorithm is based on a relaxed version of the assignment problem, where fractional assignments (over the reals) are permitted.
Mathematics Subject Classification. 68X30, 68W25, 92D25
Key words: Population biology -- kinship assignment complexity -- Tarski algebra -- phenotype space
© EDP Sciences 2007