What is the United States Swine Pathogen Database?
The US Swine Pathogen Database (US-SPD) provides genomic data to the scientific community focused on RNA viruses of swine.
It provides a web-based centralized database into which veterinary diagnostic laboratories supply input data, and from which diagnosticians and research scientists can withdraw data supporting basic and applied research on viruses infecting swine. This project has received funds from USDA-ARS (ARS Project no. 5030-32000-118-00-D), the National Pork Board (NPB Project no. 16-222), and has used resources provided by the SCINet project of the USDA-ARS (ARS Project no. 0500-00093-001-00-D).
Data types and sources
Available data types
Data in the US-SPD generally contains at a minimum four items: genomic information; date of collection; collection location (e.g., state or province); and a unique identifier. Additionally, because the bulk of the data in the database are currently Porcine reproductive and respiratory syndrome virus sequences, custom curation and annotation pipelines have determined PRRSV genotype (Type 1 or 2), the location of open reading frames and nonstructural proteins, generated amino acid sequences, and identified putative frame shifts.
The US-SPD incorporates data from public archival databases for nucleotide sequences (i.e., NCBI Genbank). Additionally, veterinary laboratories from South Dakota State University, Kansas State University, University of Minnesota, and Iowa State University are submitting sequences for curation, annotation, and dessimination on the US-SPD. The US-SPD is happy to process submissions from individual researchers to NCBI Genbank and discuss incorporation into our resource.
Genome annotation in the US-SPD
Porcine reproductive and respiratory syndrome virus sequences have been screened using custom curation and annotation pipelines to determine PRRSV genotype (Type 1 or 2), the location of open reading frames and nonstructural proteins, generated amino acid sequences, and putative frame shifts have been identified. These data may also be downloaded through the search interface.
The US-SPD uses Tripal, an open-source community genomics website toolkit.
The US-SPD makes every attempt to ensure our resource is Section 508 compliant. In the event that a resource is not accessible, please contact us and we will provide an alternative form of the requested material.
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