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Bioinformatics Advance Access published online on October 11, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl513
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received August 8, 2006
Revised September 21, 2006
Accepted October 3, 2006

Applications note

THOR: targeted high-throughput ortholog reconstructor

Matthew N. Bainbridge 1, René L. Warren 1, An He 1, Mikhail Bilenky 1, A. Gordon Robertson 1, and Steven J. M. Jones 1 *

1 British Columbia Cancer Agency (BCCA) Genome Sciences Centre, 675 West 10th Avenue Vancouver, BC, Canada

* To whom correspondence should be addressed.
Steven J. M. Jones, E-mail: sjones{at}bcgsc.ca


  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 4x 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.

Availability: THOR is implemented in java and is currently available as source code and as a web service (www.bcgsc.ca/services/thor) for reconstructing human sequences.

Associate Editor: Martin Bishop
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