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Synfind: Compiling Syntenic Regions Across Any Set Of Genomes On Demand, Haibao Tang, Matthew D. Bomhoff, Evan Briones, Liangsheng Zhang, James C. Schnable, Eric Lyons

Department of Agronomy and Horticulture: Faculty Publications

The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, evenwhennosuchgeneispresent.Thiscapabilitymeansthatsynteny-basedmethodsarefarmoreeffectivethansequencesimilaritybased methods in identifying true-negatives, a necessity forstudying gene loss and gene transposition. However, the identification of syntenicregionsrequirescomplexanalyseswhichmustberepeatedforpairwisecomparisonsbetweenanytwospecies.Therefore,as the number of published genomes increases, there is a growing demand for scalable, simple-to-use applications to perform comparative genomic analyses that cater to both gene family studies and genome-scale studies. We implemented SynFind, a web-based tool that addresses this need. Given one query genome, SynFind is capable of identifying conserved syntenic regions in any set of targetgenomes.SynFindiscapableofreportingper-geneinformation,usefulforresearchersstudyingspecificgenefamilies,aswellas genome-wide data sets of syntenic gene and predicted gene …