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cpnDB


NAR Molecular Biology Database Collection entry number 923
www.cpndb.ca
Hill, J.E.1, Penny, S.L.2, Goh, S.H.3 and Hemmingsen, S.M.4
1Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
2National Research Council Institute for Marine Biosciences, Halifax, Nova Scotia, Canada 
3Department of Pathology and Laboratory Medicine and UBC Centre for Disease Control, University of British Columbia, Vancouver, British Columbia, Canada
4National Research Council Plant Biotechnology Institute, Saskatoon, Saskatchewan, Canada

Database Description

Chaperonins are a diverse family of molecular chaperones present in the plastids, mitochondria, and cytoplasm of eukaryotes, and in bacteria and archaea. The family is divided into group I (CPN60, also known as Hsp60 or GroEL, found in bacteria, some archaea, mitochondria and plastids) and group II (CCT or TriC, found in archaea and the eukaryotic cytoplasm). Chaperonin sequences are useful for phylogenetic studies and have been widely exploited in studies of prokaryotic and eukaryotic evolution since they are often more informative than 16S rRNA sequences, especially for closely related organisms. Group I chaperonin sequences have also been employed as targets for detection and identification of organisms since a 549-567 bp segment of the cpn60 coding region, the "universal target", can be amplified with universal PCR primers. The discriminating power of cpn60 makes it an attractive target for species-specific and quantitative sequence-based diagnostics. cpnDB is a curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic, and microbial ecology studies. The database contains all available sequences for group I and group II chaperonins and the contents are updated weekly. The wealth of chaperonin sequence data available through public resources, combined with strategic efforts to generate chaperonin sequence data from taxa of particular interest or under-represented taxa has resulted in the broad taxonomic coverage of cpnDB, approximating the Ribosomal Database Project "backbone tree". The cpnDB web interface allows users to conduct text or sequence similarity searches or browse the data collection. Results of sequence similarity searches are presented as dendrograms, multiple sequence alignments or text with links to relevant records and results are easily downloaded. Sequence records are cross referenced to NCBI Genbank. cpnDB is built and maintained with open source tools.

Acknowledgements

Funding for the development and maintenance of cpnDB is provided by the National Research Council, the University of Saskatchewan and the British Columbia Centre for Disease Control.

References

1. Hill, J.E., S.L. Penny, K.G. Crowell, S.H. Goh, and S. M. Hemmingsen. (2004) cpnDB: a chaperonin sequence database. Genome Res. 14, 1669-1675.


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