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bioRxiv · 10.1101/554501

synder: inferring genomic orthologs from synteny maps

Arendsee, Z.·Wilkey, A.·Singh, U.·Li, J.·Hur, M.·Wurtele, E.
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Abstract

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 sequences 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, Z., Wilkey, A., Singh, U., Li, J., Hur, M., Wurtele, E.. 2019-02-19. synder: inferring genomic orthologs from synteny maps. https://doi.org/10.1101/554501

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