BeetleBase


19820115	BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. [PMID: 19820115] Kim HS, Murphy T, Xia J, Caragea D, Park Y, Beeman RW, Lorenzen MD, Butcher S, Manak JR, Brown SJ. 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. Nucleic Acids Res. 2010:38(Database issue) \| 105 Citations (from Europe PMC, 2025-03-22)
17090595	BeetleBase: the model organism database for Tribolium castaneum. [PMID: 17090595] Wang L, Wang S, Li Y, Paradesi MS, Brown SJ. Abstract BeetleBase (http://www.bioinformatics.ksu.edu/BeetleBase/) is an integrated resource for the Tribolium research community. The red flour beetle (Tribolium castaneum) is an important model organism for genetics, developmental biology, toxicology and comparative genomics, the genome of which has recently been sequenced. BeetleBase is constructed to integrate the genomic sequence data with information about genes, mutants, genetic markers, expressed sequence tags and publications. BeetleBase uses the Chado data model and software components developed by the Generic Model Organism Database (GMOD) project. This strategy not only reduces the time required to develop the database query tools but also makes the data structure of BeetleBase compatible with that of other model organism databases. BeetleBase will be useful to the Tribolium research community for genome annotation as well as comparative genomics. Nucleic Acids Res. 2007:35(Database issue) \| 46 Citations (from Europe PMC, 2025-03-22)

BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. [PMID: 19820115]

Kim HS, Murphy T, Xia J, Caragea D, Park Y, Beeman RW, Lorenzen MD, Butcher S, Manak JR, Brown SJ.

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.

Nucleic Acids Res. 2010:38(Database issue) | 105 Citations (from Europe PMC, 2025-03-22)

BeetleBase: the model organism database for Tribolium castaneum. [PMID: 17090595]

Wang L, Wang S, Li Y, Paradesi MS, Brown SJ.

Abstract

BeetleBase (http://www.bioinformatics.ksu.edu/BeetleBase/) is an integrated resource for the Tribolium research community. The red flour beetle (Tribolium castaneum) is an important model organism for genetics, developmental biology, toxicology and comparative genomics, the genome of which has recently been sequenced. BeetleBase is constructed to integrate the genomic sequence data with information about genes, mutants, genetic markers, expressed sequence tags and publications. BeetleBase uses the Chado data model and software components developed by the Generic Model Organism Database (GMOD) project. This strategy not only reduces the time required to develop the database query tools but also makes the data structure of BeetleBase compatible with that of other model organism databases. BeetleBase will be useful to the Tribolium research community for genome annotation as well as comparative genomics.

Nucleic Acids Res. 2007:35(Database issue) | 46 Citations (from Europe PMC, 2025-03-22)

URL:	http://www.beetlebase.org
Full name:
Description:	BeetleBase is a comprehensive sequence database and important community resource for Tribolium genetics, genomics and developmental biology.
Year founded:	2007
Last update:
Version:	V1.0
Accessibility:	Accessible
Country/Region:	United States

Data type:	DNA
Data object:	Animal
Database category:	Gene genome and annotation
Major species:	Tribolium castaneum
Keywords:	developmental biology genome annotation

University/Institution:	Kansas State University
Address:	Manhattan, KS 66506, USA
City:	Manhattan
Province/State:	KS
Country/Region:	United States
Contact name (PI/Team):	Susan J. Brown
Contact email (PI/Helpdesk):	sjbrown@ksu.edu

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Database Commons a catalog of worldwide biological databases