The Genome Reverse Compiler: an explorative annotation tool

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dc.contributor.authorWarren, Andrew S.en
dc.contributor.authorSetubal, João C.en
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentFralin Life Sciences Instituteen
dc.date.accessioned2012-08-24T11:50:25Zen
dc.date.available2012-08-24T11:50:25Zen
dc.date.issued2009-01-27en
dc.date.updated2012-08-24T11:50:25Zen
dc.description.abstractBackground As sequencing costs have decreased, whole genome sequencing has become a viable and integral part of biological laboratory research. However, the tools with which genes can be found and functionally characterized have not been readily adapted to be part of the everyday biological sciences toolkit. Most annotation pipelines remain as a service provided by large institutions or come as an unwieldy conglomerate of independent components, each requiring their own setup and maintenance. Results To address this issue we have created the Genome Reverse Compiler, an easy-to-use, open-source, automated annotation tool. The GRC is independent of third party software installs and only requires a Linux operating system. This stands in contrast to most annotation packages, which typically require installation of relational databases, sequence similarity software, and a number of other programming language modules. We provide details on the methodology used by GRC and evaluate its performance on several groups of prokaryotes using GRC's built in comparison module. Conclusion Traditionally, to perform whole genome annotation a user would either set up a pipeline or take advantage of an online service. With GRC the user need only provide the genome he or she wants to annotate and the function resource files to use. The result is high usability and a very minimal learning curve for the intended audience of life science researchers and bioinformaticians. We believe that the GRC fills a valuable niche in allowing users to perform explorative, whole-genome annotation.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Bioinformatics. 2009 Jan 27;10(1):35en
dc.identifier.doihttps://doi.org/10.1186/1471-2105-10-35en
dc.identifier.urihttp://hdl.handle.net/10919/18877en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderAndrew S Warren et al.; licensee BioMed Central Ltd.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleThe Genome Reverse Compiler: an explorative annotation toolen
dc.title.serialBMC Bioinformaticsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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