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Nucleic Acids Research Advance Access published online on October 9, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp807
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum

Hee Shin Kim1, Terence Murphy2, Jing Xia3, Doina Caragea1,3, Yoonseong Park4, Richard W. Beeman5, Marcé D. Lorenzen5, Stephen Butcher6, J. Robert Manak6,7 and Susan J. Brown1,*

1KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS 66506, 2National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, 3Department of Computer and Information Science, KSU, Manhattan, KS 66506, 4Department of Entomology, KSU, Manhattan, KS 66506, 5USDA-ARS Grain Marketing and Production Research Center, 1515 College Avenue, Manhattan KS 66502, 6Department of Biology, University of Iowa, Iowa City, IA 52242 and 7Roy J. Carver Center for Genomics, UI, Iowa City, IA 52242

*To whom correspondence should be addressed. Tel: +1 785 532 3935; Fax: +1 785 532 6653; Email: sjbrown{at}ksu.edu

Received August 14, 2009. Revised September 11, 2009. Accepted September 14, 2009.

BeetleBase (http://www.beetlebase.org) has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum. The database contains genomic sequence scaffolds mapped to 10 linkage groups (genome assembly release Tcas_3.0), genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The database was reconstructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relatational database using the Chado schema and visualized as tracks in GBrowse. The updated genetic map is visualized using the comparative genetic map viewer CMAP. To enhance the database search capabilities, the BLAST and BLAT search tools have been integrated with the GMOD tools. BeetleBase serves as a long-term repository for Tribolium genomic data, and is compatible with other model organism databases.

Present address: Marcé D. Lorenzen, Department of Entomology, North Carolina State University, Raleigh, NC 27695, USA


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