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

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...

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Bibliographic Details
Published in:Nucleic acids research 2010-01, Vol.38 (Database issue), p.D437-D442
Main Authors: Kim, Hee Shin, Murphy, Terence, Xia, Jing, Caragea, Doina, Park, Yoonseong, Beeman, Richard W, Lorenzen, Marcé D, Butcher, Stephen, Manak, J. Robert, Brown, Susan J
Format: Article
Language:English
Subjects:
Animals
Computational Biology - methods
Computational Biology - trends
Databases, Genetic
Databases, Nucleic Acid
Databases, Protein
Expressed Sequence Tags
Genome
Genomics
Information Storage and Retrieval - methods
Internet
Models, Genetic
Protein Structure, Tertiary
Software
Tribolium - genetics
Tribolium castaneum
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Summary: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.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkp807