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BeetleBase in 2010: Revisions to Provide Comprehensive Genomic Information for Tribolium Castaneum

Overview
Journal Nucleic Acids Res
Publisher Oxford University Press
Specialty Biochemistry
Date 2009 Oct 13
PMID 19820115
Citations 92
Authors
Hee Shin Kim
Terence Murphy
Jing Xia
Doina Caragea
Yoonseong Park
Richard W Beeman
Marce D Lorenzen
Stephen Butcher
J Robert Manak
Susan J Brown
Affiliations
Soon will be listed here.
Abstract

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.

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