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Tuesday, June 28 • 3:10pm - 4:25pm
P07: Hardwood Genomics Database (HGD): a web portal and database resource for hardwood tree genomic and genetic research

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Poster    doi:10.7490/f1000research.1112718.1

Authors

  • Ming Chen, University of Tennessee at Knoxville, TN;
  • Nathan Henry, University of Tennessee at Knoxville, TN;
  • John Carlson, Pennsylvania State University, University Park, PA, USA;
  • Meg Staton, University of Tennessee at Knoxville, TN; 
Abstract
The Hardwood Genomics Database (HGD, www.hardwoodgenomics.org) serves forest tree scientists by providing online access to hardwood tree genomic and genetic data. HGD currently houses data for economically and phylogenetically important hardwood species including assembled reference genomes, transcriptomes, and genetic mapping information. The results of bioinformatic analysis including functional annotation of genes, ontology assignment, analysis of gene expression patterns across RNASeq libraries and simple sequence repeat (SSR) identification are available to enhance the utility of the information. The web site provides access to online tools for mining and visualization of these data sets, including BLAST for comparing sequences, Jbrowse1 for browsing genomes, Apollo2 for community annotation and SyMAP3 for comparative genomics. However, these tools are limited in scope. To maximize the ability for users of community databases to harness this information and perform their own custom analysis, we are collaborating with other genome databases to build an interface to the Galaxy data analysis platform4. Users will be able to select and transfer data from the HGD to a Galaxy instance or run a pre-designed Galaxy workflow on selected datasets. 

Presenters
avatar for Margaret Staton

Margaret Staton

University of Tennessee Knoxville
My lab works on genome databases, web applications, cyberinfrastructure, and RNASeq data. Our main website is hardwoodgenomics.org.


Attendees (4)