Genetics, Development and Cell Biology, Agronomy, Center for Metabolic Biology
Journal or Book Title
Ortholog inference is a key step in understanding the evolution and function of a gene or other genomic feature. Yet often no similar sequence can be identified, or the true ortholog is hidden among false positives. A solution is to consider the sequence's genomic context. We present the generic program, synder, for tracing features of interest between genomes based on a synteny map. This approach narrows genomic search-space independently of the sequence of the feature of interest. We illustrate the utility of synder by finding orthologs for the Arabidopsis thaliana 13-member gene family of Nuclear Factor YC transcription factor across the Brassicaceae clade.
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Arendsee, Zebulun; Wilkey, Andrew; Singh, Urminder; Li, Jing; Hur, Manhoi; and Wurtele, Eve Syrkin, "synder: inferring genomic orthologs from synteny maps" (2019). Genetics, Development and Cell Biology Publications. 209.