This project's overarching aim is to develop a flexible and extensible infrastructure that will allow the entire community of a given organism to easily contribute to the genome annotation process. We are doing this by integrating and significantly enhancing the functionality existing GMOD tools: Apollo, used for the creation of genomic feature annotations tied to specific locations on the DNA sequence;the Distributed Annotation System (DAS) protocol and associated software, which supports the exchange of annotations over the Internet between researchers;and Generic Genome Browser (GBrowse), used for displaying genome annotations on interactive Web pages. We are combining these applications and building on them to create a novel web-based infrastructure that will offer robust, easy-to-use tools for collaborative, community- driven genome feature annotation by a much broader community of users.
As the number of whole genomes being sequenced increases the annotation of these genomes-what genes are present, the locations of promoter and enhancer sites, and other features-has become the rate- limiting step. Current annotations are unreliable, difficult to compare, and in some cases non-existent. This has serious consequences, because it diminishes the utility of these genome sequences, particularly as they are used for improving the standard of annotation of the human genome which is essential for its maximal exploitation.
|Schoville, Sean D; Chen, Yolanda H; Andersson, Martin N et al. (2018) A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Sci Rep 8:1931|
|Harper, Lisa; Campbell, Jacqueline; Cannon, Ethalinda K S et al. (2018) AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database (Oxford) 2018:|
|Poynton, Helen C; Hasenbein, Simone; Benoit, Joshua B et al. (2018) The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. Environ Sci Technol 52:6009-6022|
|Papanicolaou, Alexie; Schetelig, Marc F; Arensburger, Peter et al. (2017) Erratum to: The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. Genome Biol 18:11|
|Putman, Tim E; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian et al. (2017) WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata. Database (Oxford) 2017:|
|Buels, Robert; Yao, Eric; Diesh, Colin M et al. (2016) JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol 17:66|
|Lee, Eduardo; Helt, Gregg A; Reese, Justin T et al. (2013) Web Apollo: a web-based genomic annotation editing platform. Genome Biol 14:R93|
|Lee, Ed; Harris, Nomi; Gibson, Mark et al. (2009) Apollo: a community resource for genome annotation editing. Bioinformatics 25:1836-7|