Efficient haplotype block recognition of very long and dense genetic sequences.

ABSTRACT:

Background

The new sequencing technologies enable to scan very long and dense genetic sequences, obtaining datasets of genetic markers that are an order of magnitude larger than previously available. Such genetic sequences are characterized by common alleles interspersed with multiple rarer alleles. This situation has renewed the interest for the identification of haplotypes carrying the rare risk alleles. However, large scale explorations of the linkage-disequilibrium (LD) pattern to identify haplotype blocks are not easy to perform, because traditional algorithms have at least Θ(n2) time and memory complexity.

Results

We derived three incremental optimizations of the widely used haplotype block recognition algorithm proposed by Gabriel et al. in 2002. Our most efficient so

SUBMITTER: Taliun D 

PROVIDER: S-EPMC3898000 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature