synder: inferring genomic orthologs from synteny maps

Date
2019-02-19
Authors
Arendsee, Zebulun
Wilkey, Andrew
Singh, Urminder
Li, Jing
Hur, Manhoi
Wurtele, Eve Syrkin
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Agronomy
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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 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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This is a pre-print made available through bioRxiv at doi: 10.1101/554501.

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