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Nucleic Acids Res. 2015 Jan;43(Database issue):D714-9. doi: 10.1093/nar/gku983. Epub 2014 Oct 20.

The i5k Workspace@NAL--enabling genomic data access, visualization and curation of arthropod genomes.

Author information

1
National Agricultural Library, Beltsville, MD 20705, USA monica.poelchau@ars.usda.gov.
2
National Agricultural Library, Beltsville, MD 20705, USA christopher.childers@ars.usda.gov.
3
National Agricultural Library, Beltsville, MD 20705, USA.
4
Bee Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705, USA.
5
National Agricultural Library, Beltsville, MD 20705, USA Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan.
6
National Agricultural Library, Beltsville, MD 20705, USA Graduate Institute of Electrical Engineering, National Taiwan University, Taipei 10617, Taiwan.
7
Crop Production and Protection, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705, USA.

Abstract

The 5000 arthropod genomes initiative (i5k) has tasked itself with coordinating the sequencing of 5000 insect or related arthropod genomes. The resulting influx of data, mostly from small research groups or communities with little bioinformatics experience, will require visualization, dissemination and curation, preferably from a centralized platform. The National Agricultural Library (NAL) has implemented the i5k Workspace@NAL (http://i5k.nal.usda.gov/) to help meet the i5k initiative's genome hosting needs. Any i5k member is encouraged to contact the i5k Workspace with their genome project details. Once submitted, new content will be accessible via organism pages, genome browsers and BLAST search engines, which are implemented via the open-source Tripal framework, a web interface for the underlying Chado database schema. We also implement the Web Apollo software for groups that choose to curate gene models. New content will add to the existing body of 35 arthropod species, which include species relevant for many aspects of arthropod genomic research, including agriculture, invasion biology, systematics, ecology and evolution, and developmental research.

PMID:
25332403
PMCID:
PMC4384035
DOI:
10.1093/nar/gku983
[Indexed for MEDLINE]
Free PMC Article

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