Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes
Rahul V Rane, John G Oakeshott, Thu Nguyen, Ary A Hoffmann, Siu F Lee
BMC GENOMICS | BMC | Published : 2017
BACKGROUND: Distinguishing orthologous and paralogous relationships between genes across multiple species is essential for comparative genomic analyses. Various computational approaches have been developed to resolve these evolutionary relationships, but strong trade-offs between precision and recall of orthologue prediction remains an ongoing challenge. RESULTS: Here we present Orthonome, an orthologue prediction pipeline, designed to reduce the trade-off between orthologue capture rates (recall) and accuracy of multi-species orthologue prediction. The pipeline compares sequence domains and then forms sequence-similar clusters before using phylogenetic comparisons to identify inparalogues. ..View full abstract
This work was funded by the Australian Science and Industry Endowment Fund (SIEF) and a NeCTAR computation grant to RVR. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.