THOR: targeted high-throughput ortholog reconstructor.

by: MN Bainbridge, RL Warren, A He, M Bilenky, AG Robertson, SJ Jones

Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2622-2624.

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Abstract

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.

@article{citeulike:2291788, abstract = {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.}, address = {British Columbia Cancer Agency (BCCA) Genome Sciences Centre, 675 West 10th Avenue, Vancouver, BC, Canada. matthewb@bcgsc.ca}, author = {Bainbridge, M. N. and Warren, R. L. and He, A. and Bilenky, M. and Robertson, A. G. and Jones, S. J. }, citeulike-article-id = {2291788}, issn = {1460-2059}, journal = {Bioinformatics}, month = {October}, number = {19}, pages = {2622--2624}, posted-at = {2008-01-26 06:40:12}, priority = {2}, title = {THOR: targeted high-throughput ortholog reconstructor.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/17038343}, volume = {23}, year = {2007} }

RIS record

TY - JOUR ID - citeulike:2291788 L3 - citeulike-article-id:2291788 TI - THOR: targeted high-throughput ortholog reconstructor. JF - Bioinformatics VL - 23 IS - 19 SP - 2622 EP - 2624 AD - British Columbia Cancer Agency (BCCA) Genome Sciences Centre, 675 West 10th Avenue, Vancouver, BC, Canada. matthewb@bcgsc.ca SN - 1460-2059 N2 - 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. AU - Bainbridge, MN AU - Warren, RL AU - He, A AU - Bilenky, M AU - Robertson, AG AU - Jones, SJ PY - 2007/10/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/17038343 ER -

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