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synder: inferring genomic orthologs from synteny maps

View ORCID ProfileZebulun Arendsee, View ORCID ProfileAndrew Wilkey, View ORCID ProfileUrminder Singh, View ORCID ProfileJing Li, View ORCID ProfileManhoi Hur, View ORCID ProfileEve Syrkin Wurtele
doi: https://doi.org/10.1101/554501
Zebulun Arendsee
1Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA, 50010, USA
2Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
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Andrew Wilkey
3Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA
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Urminder Singh
1Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA, 50010, USA
2Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
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Jing Li
1Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA, 50010, USA
2Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
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Manhoi Hur
1Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA, 50010, USA
2Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
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Eve Syrkin Wurtele
1Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA, 50010, USA
2Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
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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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Posted February 19, 2019.
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synder: inferring genomic orthologs from synteny maps
Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, Eve Syrkin Wurtele
bioRxiv 554501; doi: https://doi.org/10.1101/554501
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synder: inferring genomic orthologs from synteny maps
Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, Eve Syrkin Wurtele
bioRxiv 554501; doi: https://doi.org/10.1101/554501

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