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

Hee Shin Kim; Terence Murphy; Jing Xia; Doina Caragea; Yoonseong Park; Richard W Beeman; Marcé D Lorenzen; Stephen Butcher; J Robert Manak; Susan J Brown

doi:10.1093/nar/gkp807

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

Journal article

Open access

Peer reviewed

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

Hee Shin Kim, Terence Murphy, Jing Xia, Doina Caragea, Yoonseong Park, Richard W Beeman, Marcé D Lorenzen, Stephen Butcher, J Robert Manak and Susan J Brown

Nucleic acids research, Vol.38(Database issue), pp.D437-D442

01/2010

DOI: 10.1093/nar/gkp807

PMCID: PMC2808946

PMID: 19820115

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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.

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

Details

Title: Subtitle: BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum
Creators: Hee Shin Kim - KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
Terence Murphy
Jing Xia
Doina Caragea
Yoonseong Park
Richard W Beeman
Marcé D Lorenzen
Stephen Butcher
J Robert Manak
Susan J Brown
Resource Type: Journal article
Publication Details: Nucleic acids research, Vol.38(Database issue), pp.D437-D442
DOI: 10.1093/nar/gkp807
PMID: 19820115
PMCID: PMC2808946
NLM abbreviation: Nucleic Acids Res
ISSN: 0305-1048
eISSN: 1362-4962
Grant note: Intramural NIH HHS P20 RR016475 / NCRR NIH HHS R01 HD029594 / NICHD NIH HHS R01 HD029594-18 / NICHD NIH HHS
Language: English
Date published: 01/2010
Academic Unit: Stead Family Department of Pediatrics; Biology; Craniofacial Anomalies Research Center
Record Identifier: 9984217422702771

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