THOR: Targeted high-throughput ortholog reconstructor

Abstract

Summary: Low-coverage genomes (LCGs) are becoming an increasingly important source of data for phylogenetic studies. However, assembly of these genomes is time consuming, difficult and lags behind sequence generation. THOR is a fast, stringent application for targeted reconstruction of sequence orthologs in unassembled LCGs. Using a 4× coverage set of mouse whole-genome sequence reads, THOR could partially or completely reconstruct 416/1000 human promoter ortholog regions in ∼7.3 min/promoter. THOR's reconstruction rate improves markedly with both higher-coverage, and less divergent target species. © The Author 2006. Published by Oxford University Press. All rights reserved.