Nasonia vitripennis. ©Oliver Niehuis

Important: HGD has been reorganized. Please read about updates below.

HGD Updates (June 5, 2020)

The HGD website has been updated and revamped. HGD data content is no longer separated into the three original divisions (BeeBase, NasoniaBase and the Ant Genomes Portal), but is now consolidated into one unified site. Use the Archive pull-down menu above to access data from one of the original websites, which will remain available but will no longer be updated.

The current content of HGD is based on a date freeze data of April 4, 2019. We anticipate an update in Fall 2020 based on a May 2020 data freeze.

The JBrowse pull-down menu provides browsers for all species listed in HymenopteraMine v1.4 Data Sources, except unpublished genomes currently being annotated at the i5K Workspace@NAL. The assembly releases in JBrowse correspond with the April 2019 data freeze.

The new HGD BLAST server allows you to search genome assemblies and view your blast hits in JBrowse. The HGD BLAST server currently does not provide search databases for proteins, coding sequences or transcripts. Since most of these genomes are available at NCBI, you can use NCBI BLAST after specifying an organism (under "BLAST Genomes") to search proteins and transcripts. Contact us if this is a problem for you.

The "Contributing Data" tab provides information on how you can contribute datasets for incorporation into a future release of HGD JBrowse or HymenopteraMine.

HGD BACKGROUND

The Hymenoptera Genome Database is a genome informatics resource that supports the research of insects of the order Hymenoptera (e.g. bees, wasps, ants). HGD provides tools for data mining (HymenopteraMine), sequence searching (BLAST), genome browsing (JBrowse), genome annotation (Apollo) and data download.

HymenopteraMine is a data mining tool that integrates all of the genomes in HGD with biological data from a variety of sources. The goal of HymenopteraMine is to accelerate genomics analysis by enabling researchers without scripting skills to create and export customized annotation datasets merged with their own research data for use in downstream analyses. HymenopteraMine facilitates cross-species data mining based on orthology and supports meta-analyses by tracking identifiers across gene sets and genome assemblies.

A chapter on Hymenoptera Genome Database in the Methods in Molecular Biology volume "Eukaryotic Genomic Databases" focuses on HymenopteraMine:

Elsik C.G., Tayal A., Unni D.R., Burns G.W., Hagen D.E. (2018) Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects. In: Kollmar M. (eds) Eukaryotic Genomic Databases. Methods in Molecular Biology, vol 1757. Humana Press, New York, NY. doi: 10.1007/978-1-4939-7737-6_17

Click here to download a free preprint.

How to Cite:

1) Cite the use of HGD and HymenopteraMine with the most recent HGD publication:

Elsik CG, Tayal A, Diesh CM, Unni DR, Emery ML, Nguyen HN, Hagen DE. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. Nucleic Acids Research 2016 Jan 4;44(D1):D793-800. doi: 10.1093/nar/gkv1208. Epub 2015 Nov 17. PubMed PMID: 26578564.

2) Cite the appropriate consortium publication for the genome you used.

Please contact us if you have any questions or suggestions for HGD.