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dc.contributor.authorDoran, Anthony G
dc.contributor.authorCreevey, Christopher J.
dc.date.accessioned2013-05-21T14:49:42Z
dc.date.available2013-05-21T14:49:42Z
dc.date.issued2013-02-08
dc.identifier.citationDoran, Anthony G. and Creevey, Christopher J. Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms. BMC Bioinformatics 2013, 14:45 doi:10.1186/1471-2105-14-45en_GB
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/11019/402
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2105-14-45
dc.identifier.urihttp://www.biomedcentral.com/1471-2105/14/45
dc.descriptionpeer-revieweden_GB
dc.descriptionpeer-reviewed
dc.description.abstractBackground: Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Results: Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. Conclusions: SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience.en_GB
dc.description.sponsorshipTeagasc Walsh Fellowship Scheme; Science Foundation Ireland (SFI) Stokes lecturer scheme (number: 07/SK/B1236A)en_GB
dc.language.isoenen_GB
dc.publisherBiomed Central
dc.relation.ispartofseriesBMC Bioinformatics;vol 14
dc.subjectSNPs
dc.subjectAnnotation
dc.subjectSoftware
dc.subjectNon-model organisms
dc.titleSnpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organismsen_GB
dc.typeArticleen_GB
refterms.dateFOA2018-01-12T07:59:19Z


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