NRSP-8 Animal Bioinformatics 2012: Update

The NRSP-8 Bioinformatics Coordination Program (2008-2013) has made significant progress in 2012 in terms of creating shared genomic tools, reagents, and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest. Our accomplishments included assisting community members with their individual needs, as well as the development and expansion of databases and tools to harvest, share, and disseminate valuable genomics information (http://www.animalgenome.org). In brief, 2552 new cattle, chicken, pig, sheep, and rainbow trout QTL have been curated, and several new functions added to the Animal QTLdb. For instance, 770k high-density SNP and 4.1M dbSNP data were made available both in GBrowse to align with QTL and in SNPlotz for genome analysis; and mapping of animal traits to Vertebrate Trait Ontology (VT), Product Trait Ontology (PT) and Clinical Measurement Ontology (CMO) has facilitated QTL comparisons by trait ontology in VCMap. We have also worked with iPlant to develop customized pipelines for animal sequence data sets. In addition to the development and maintenance of new tools, the web portals for cattle, pig, sheep, and aquaculture species have been kept up-to-date to facilitate community activities. For example, a new listserv was set up specifically for sheep researchers (SheepModels), and over 170 new subscribers were added to ANGENMAP, for which the listserv activity has reached an unprecedented nearly 500 emails per year. We have kept the community informed of our progress via periodic “what’s new” letters electronically posted to over 2300 people.