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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Improvement of Hard Winter Wheat to Biotic and Abiotic Stresses

Location: Hard Winter Wheat Genetics Research Unit

Title: SNPMeta: SNP annotation and SNP metadata collection without a reference genome

Authors
item Kono, Thomas -
item Kiran, Seth -
item Poland, Jesse
item Morrell, Peter -

Submitted to: Molecular Ecology Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 9, 2013
Publication Date: November 16, 2013
Repository URL: http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12183/pdf
Citation: Kono, T., Kiran, S., Poland, J.A., Morrell, P. 2013. SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Molecular Ecology Resources. 14, 419-425.

Interpretive Summary: To utilize genome sequence information to make inference to biological traits' it is important to have genes annotated in sequence databases. For model organisms (i.e. mouse, fly, rice) this is readily accomplished through large efforts centered on the reference genome sequence. For other species that do not have sufficient reference genome resources this approach is limited. Further, the increasing availability for low-cost DNA sequencing is making new datasets readily available. To fully leverage these sequence dataset it is important to have user-friendly tools available for annotation. Here we present a bioinformatics tool SNPMeta that gathers information about DNA polymorphisms found in sequencing datasets and compares these sequences to reference databases for characterization and annotation.

Technical Abstract: The increase in availability of resequencing data is greatly accelerating SNP discovery and has facilitated the development of SNP genotyping assays. This, in turn, is increasing interest in annotation of individual SNPs. Currently, these data are only available through curation, or comparison to a reference genome. However, some organisms serve as important genetic models despite the lack of a reference genome. For these species, it is possible to annotate SNPs through comparison to cDNA, or data from well annotated genes in public repositories. We present a tool, SNPMeta, which gathers information about SNPs by comparison to sequences present in GenBank databases. Because SNPMeta sources information from GenBank, it can be used to annotate SNPs in non-model species, or species that lack a reference genome.

Last Modified: 9/10/2014
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