THOR: targeted high-throughput ortholog reconstructor.
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 4x coverage set of mouse whole-genome sequence reads, THOR could partially or completely reconstruct 416/1000 human promoter ortholog regions in approximately 7.3 min/promoter. THOR's reconstruction rate improves markedly with both higher-coverage, and less divergent target species.
Bainbridge
Matthew N
MN
British Columbia Cancer Agency (BCCA) Genome Sciences Centre, 675 West 10th Avenue, Vancouver, BC, Canada. matthewb@bcgsc.ca
Warren
René L
RL
He
An
A
Bilenky
Mikhail
M
Robertson
A Gordon
AG
Jones
Steven J M
SJ
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D018390:Gene Targeting / Q000379:methods*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software