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THOR: targeted high-throughput ortholog reconstructor.

Matthew N Bainbridge·René L Warren·An He·Mikhail Bilenky·A Gordon Robertson·Steven J M Jones
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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.

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AlgorithmsBase SequenceChromosome MappingGene TargetingGenome, HumanHumansMolecular Sequence DataProgramming LanguagesSequence AlignmentSequence Analysis, DNASequence Homology, Nucleic AcidSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

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Matthew N Bainbridge, René L Warren, An He, Mikhail Bilenky, A Gordon Robertson, Steven J M Jones. 2006-10-11. THOR: targeted high-throughput ortholog reconstructor.. https://doi.org/10.1093/bioinformatics%2Fbtl513

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