Agrigenomic research.
Raise your expectations.

Discover more, save time, eliminate hassle with the most powerful and user-friendly software for plant and animal genetics.

Accurate prediction of genetic merit. Marker-assisted breeding. Increased production levels. Improving the value of crops and livestock in today's world requires an in-depth understanding of genetic variation and how it relates to traits of interest. Such understanding starts with high quality data. But it's made possible through powerful analytics. You paid good money for your data. Now you can take advantage of all it has to offer.

Introducing SNP & Variation Suite 7 for agricultural genetic research. SVS 7 delivers world-class analytic tools in a user-friendly, yet extraordinarily powerful interface. No more struggling to coerce command-line software -- designed exclusively for human genetics -- to work for the plant or animal species you're studying. SVS 7 supports a wide-variety of species enabling you to quickly and easily identify variants related to pest and disease resistance, increased feed efficiency, milk production, and more.

It's time to raise your expectations for what software can do for your research.

Agrigenomic Advantages »    |    Resources »    |    Download a free trial of SVS »

Support for a Wide Variety of Plant and Animal Genomes Animal Bos taurus - UMD3.1, Btau_4.0,   Btau_4.6.1 Caenorhabditis elegans - WS_190 Canis familiaris - BROADD_2 Danio rerio - ZFISH_7 Drosophila melanogaster - BDGP_5.4 Equus caballus – EquCab_2 Gallus gallus - ICGSC_4,    WASHUC_2 Macaca mulatta - MMUL_1 Mus musculus - NCBIM_37 Ovis aries - OAR 1.0, OAR_2.0,   OAR_3.1 Rattus norvegicus - RGSC_3.4 Sus scrofa - Sscrofa_9.2, Sscrofa_10.2 Plant Arabidopsis thaliana - TAIR_9 Brassica rapa - JGI_1.2 Eucalyptus gradis - JGI_1.1 Glycine max - JGI_Glyma1.1 Oryza sativa - MSU_6, MSU_7 Saccharomyces cerevisiae - SGD_1 Schizosaccharomyces pombe - EF_1 Setaria italica - JGI_2.1 Sorghum bicolor - Sbi_1 Zea mays - AGP_1, AGP_2 With more added frequently! Any genome and corresponding annotations can easily be added, if available.

User-friendly design supporting a wide-variety of species and genomes

No more coercing software designed for human genetics to work with the plant or animal species you're studying. SVS supports a wide-variety of species, including different genomic builds for some. If your particular species is not included by default, you can easily add it along with corresponding annotations from a point-and-click interface. And switching between species and genomes is easy too. Just select the species you're studying from the project options tab or from a drop down menu in the genome browser and you're ready to go.

Powerful visualizations reveal hot spots and differences among breeds

All visualizations in SVS are dynamic, interactive, and integrative so you can quickly identify hot spots and navigate to areas of interest. Compare variant maps, LD structure, or copy number patterns among breeds. Produce Manhattan plots for any number of dependent variables. Assess identity by descent or population stratification to locate problematic samples. The best part: any genomic-based plot can be visualized in an interactive genome browser alongside relevant annotations with proper genomic coordinates for the species you're studying.

Discover more by analyzing multiple data types in the same package

SNP, CNV, or sequence data. Case-control or quantitative traits. Single marker or multi-marker analyses. Population or pedigree-based studies. All are supported. SVS provides the most complete set of statistical and visual analytic tools to help you quickly identify genetic variants or haplotypes and their association with traits of interest. Not to mention all the time you'll save by not having to move large, complex data sets between multiple packages.

Unrivaled speed on any size data

Candidate genes or whole genome. Microarrays or next-generation sequencing. SVS delivers unparalleled performance on any size data. Seamlessly navigate spreadsheets with billions of data points. Plot variant maps, heat maps, and genomic annotations across the entire genome for thousands of samples. Perform association tests in seconds. You'll be amazed. We promise.

No more command-line (unless you want to)

SVS is incredibly powerful and flexible with a user-friendly interface on the front-end and a fully-programmatic access on the back-end. So whether you're one who shudders at the thought of writing another line of code, or one who lives for it, SVS empowers you to do more than you ever thought possible.

Spend less time fighting with data and more time doing science

It's no secret that more time on any analysis project is spent preparing, manipulating, and formatting data than the actual analysis. This realization is undoubtedly more profound with plant and animal studies given the limited software available that works with non-human genomes. SVS supports the broadest array of data formats for both import and export, eliminating the hassles of working with large data. You'll also find a host of tools that make it easy to format and recode data, merge data sets, create subsets, and more.

Comprehensive QC delivers higher quality results

High quality data is critical to high quality results. To ensure your data is of the highest quality SVS 7 provides the most comprehensive set of quality assurance tools helping you not only assess the quality of your data, but remedy any problems as well.

Case Studies Gonzalo Rincon, DVM is a Project Scientist in the Medrano Lab, part of the Department of Animal Science, at the University of California, Davis. While the lab works on several diff erent species including canine and ovine, the main focus is bovine research. Rincon is in charge of the analysis, and his goal is to find SNP and CNV variations that affect phenotypes such as the quality of milk and beef. Through the use of tools from Golden Helix, Rincon and his colleagues have been able to publish 14 papers and obtain 2 patents, three-to-four times faster than they would have been able to.    View Dr. Rincon's case study » The International Maize and Wheat Improvement Center's (CIMMYT) mission is "To sustainably increase the productivity of maize and wheat systems to ensure global food security and reduce poverty." To accomplish this task, one area of focus for the CIMMYT is genetic research and molecular marker technology to improve certain traits of maize and wheat, such as drought tolerance, resistance to disease, and amino acid balance. In this case study, Dr. Raman Babu describes his experience using SVS to analyze model populations in order to predict certain traits at CIMMYT.    Download Dr. Babu's case study » Dr. Matthew McClure is a Research Geneticist at The Bovine Functional Genomics Lab at the USDA-ARS. In this webcast, Dr. McClure describes his current research in agrigenomics, the technologies and methods he is using to identify causal mutations for Mendelian and complex traits, and how SVS has sped up the pace of discovery. View Dr. McClure's webcast »		Selected Agrigenomic Publications Bovine Wickramasinghe, S et al. (2011) Variants in the pregnancy-associated plasma protein-A2 gene on Bos taurus autosome 16 are associated with daughter calving ease and productive life in Holstein cattle. Journal of Dairy Science, 94(3):1552-1558, doi:10.3168/jds.2010-3237. Abstract Rincon, G et al. (2009) Fine mapping and association analysis of a quantitative trait locus for milk production traits on Bos taurus autosome 4. Journal of Dairy Science, 92:758-764. doi:10.3168/jds.2008-1395. Abstract Canine Rincon, G et al. (2011) Comparison of buccal and blood-derived canine DNA, either native or whole genome amplified, for array-based genome-wide association studies. BMC Research Notes, 4:226, doi:10.1186/1756-0500-4-226. Abstract Equine Go, Y et al. (2011) Genome-Wide Association Study Among Four Horse Breeds Identifies a Common Haplotype Associated with the In Vitro CD3+ T Cell Susceptibility/Resistance to Equine Arteritis Virus Infection. Journal of Virology, doi:10.1128/JVI.06068-11. Abstract Plant Dillon, S et al. (2010) Allelic Variation in Cell Wall Candidate Genes Affecting Solid Wood Properties in Natural Populations and Land Races of Pinus radiata. Genetics, doi:10.1534/genetics.110.116582. Abstract Emanuelli, F et al. (2010) A candidate gene association study on muscat flavor in grapevine (Vitis vinifera L.). BMC Plant Biology, 10:241, doi:10.1186/1471-2229-10-241. Abstract View all Golden Helix journal article citations »
Other Resources Creating a Genome Map in SVS While there are numerous genome maps available in SVS, you may find it necessary to create your own. It is a simple and straightforward process to create a map once you've found the pertinent data elsewhere. Learn how using our interactive tutorial » Calculating the Inbreeding Coefficient Inbreeding is a common problem in plant and animal genomic analysis. To help determine if this is a factor in your study, SVS comes equipped with the ability to calculate the inbreeding coefficient for each sample respresented in your data. Find out more in our manual » View a complete list of resources »		Customer Support The Golden Helix Support Team is here to help you succeed. Our top priority is to make sure that the Golden Helix software is installed and working properly on your computer and that you have the tools you need to complete your research. Contact us at: Hours: Monday through Friday, 9:00 am - 5:00 pm MST Email: support@goldenhelix.com Phone: +1 (406) 585-8137 Toll Free: +1 (888) 589-4629