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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #342944

Research Project: MaizeGDB: Enabling Access to Basic, Translational, and Applied Research Information

Location: Corn Insects and Crop Genetics Research

Title: SNPversity: A web-based tool for visualizing diversity

Author
item Schott, David - Iowa State University
item Vinnakota, Abhinav - Iowa State University
item Portwood, John
item Andorf, Carson
item Sen, Taner

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/20/2018
Publication Date: 4/20/2018
Citation: Schott, D.A., Vinnakota, A.G., Portwood II, J.L., Andorf, C.M., Sen, T.Z. 2018. SNPversity: A web-based tool for visualizing diversity. Database: The Journal of Biological Databases and Curation. doi:10.1093/database/bay037.
DOI: https://doi.org/10.1093/database/bay037

Interpretive Summary: With the improved affordability of sequencing methods, there has become a large amount of sequence data available for plant species. This data is invaluable in understanding the diversity of a species, but web-based tools to process and visualize this type of data is lacking. We developed a web-based tool called SNPversity that allows users to navigate and visualize changes in DNA across many different maize lines. This tool was developed for maize but could be extended to other crop species like soybean, sorghum, wheat, barley, rye, and oat. This tool is open-source and available here: http://www.maizegdb.org/snpversity.

Technical Abstract: Background: Many stand-alone desktop software suites exist to visualize single nucleotide polymorphisms (SNP) diversity, but web-based software that can be easily implemented and used for biological databases is absent. SNPversity was created to answer this need by building an open-source visualization tool that can be implemented on a unix-like machine and served through a web browser that can be accessible worldwide. Methods: SNPversity consists of a HDF5 database back-end for SNPs, a data exchange layer powered by TASSEL libraries that represent data in JSON format, and an interface layer using PHP to visualize SNP information. SNPversity displays data in real-time through a web browser in grids that are color-coded according to a given SNP’s allelic status and mutational state. Results: SNPversity is currently available at MaizeGDB (https://www.maizegdb.org), the maize community’s database, and will be soon available at GrainGenes (https://wheat.pw.usda.gov, https://www.graingenes.org), the clade-oriented database for Triticeae and Avena species, including wheat, barley, rye, and oat. The code and documentation are uploaded onto github, and they are freely available to the public. We expect that the tool will be highly useful for other biological databases with a similar need to display SNP diversity through their web interfaces.