Generic number systems and haplotype analysis

Abstract

Three simple and elegant algorithms involving binary and mixed-radix numbers are presented as C subroutines and applied to gene-counting procedure. The first, a multikey radix-sorting subroutine, is used to tally individuals with similar genetic marker information. The second, a subroutine for N-ary number addition, is used to enumerate all possible phases of a heterozygote. The third, a mixed-radix number subroutine, is used to generate all haplotypes and indexing single array of haplotype frequencies. Examples exposing these algorithms are also given. The sorting algorithm entails broad application while the N-ary and mixed-radix number algorithms are very efficient for generic looping. Implementation of gene-counting using these algorithms avoids use of multilocus genotype identifier and improves its portability to other analysis. © 2002 Elsevier Science Ireland Ltd. All rights reserved.