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THOR: targeted high-throughput ortholog reconstructor.

Matthew N Bainbridge¹, René L Warren, An He

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

Bioinformatics (Oxford, England)

|October 14, 2006

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THOR is a new tool that rapidly reconstructs gene sequences from low-coverage genomes, aiding phylogenetic studies. It efficiently targets ortholog regions, improving data accessibility for evolutionary research.

Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Low-coverage genomes (LCGs) are valuable for phylogenetic analysis but challenging to assemble.
Current genome assembly methods are slow and complex, hindering rapid data utilization.

Purpose of the Study:

To introduce THOR, a novel bioinformatics application designed for efficient targeted reconstruction of sequence orthologs.
To demonstrate THOR's capability in assembling specific genomic regions from unassembled LCGs.

Main Methods:

THOR application utilizes a stringent, targeted approach for sequence ortholog reconstruction.
Tested on a 4x coverage mouse whole-genome dataset to reconstruct human promoter ortholog regions.

Main Results:

Related Experiment Videos

THOR successfully reconstructed 416 out of 1000 targeted human promoter ortholog regions.
Reconstruction time averaged approximately 7.3 minutes per promoter region.
Reconstruction efficiency increases with higher genome coverage and lower species divergence.

Conclusions:

THOR offers a fast and effective solution for analyzing LCGs, particularly for targeted phylogenetic reconstruction.
The application accelerates the use of genomic data in evolutionary studies by overcoming assembly bottlenecks.