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 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.
Kim
Hee Shin
HS
KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
Murphy
Terence
T
Xia
Jing
J
Caragea
Doina
D
Park
Yoonseong
Y
Beeman
Richard W
RW
Lorenzen
Marcé D
MD
Butcher
Stephen
S
Manak
J Robert
JR
Brown
Susan J
SJ
D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D020224:Expressed Sequence Tags; D016678:Genome; D023281:Genomics; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D008957:Models, Genetic; D017434:Protein Structure, Tertiary; D012984:Software; D014231:Tribolium / Q000235:genetics*