PRABI
Rhone-Alpes Bioinformatics Center


PRABI : LBBE

BIBIDB

BIBIDB is a nomenclature and taxinomy driven bacterial DNA sequences database used in bacteria identification

Construction is done by the following process :
- a taxonomic and nomenclature compliant database is automatically cross compiled from informations maintained by DSMZ team (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH) and J-P. Euzeby’s List of Bacterial names with Standing in Nomenclature LBSN. Type strains (TS) are tagged. Informations are saved in a PostgreSQL database.
- ACNUC iterative queries on GenBank are constructed using this taxonomy and nomenclature database to extract only strains bearing a name with standing in Nomenclature i.e striclty in accordance with the International Code of Nomenclature of Bacteria (see EUZEBY (J.P.) : List of bacterial names with standing in nomenclature : a folder available on the Internet. Int. J. Syst. Bacteriol., 1997, 47, 590-592.)
- Sequences and informations are formated for further use. From a list of discrepancies between taxinomy and phylogeny reported by microbiologists, sequences considered as ill identified are tagged (X). Type strains are explicitly identified (T).

BIBIDB contains a set of specialized banks gathering genes belonging to well-known families : rRNA, hsp65, sod, rpob etc. Databases are either nomenclature "stringent" (sequences are selected according to their standing in nomencalture) or "lax" (in this case all the sequences are maintained in the bank). Type strains only bank are constructed for major genes.

The result is a specialized sequence database that may be queried by a webtool BIBI to fulfill identification tasks in microbiological laboratories.

This database is different from the previous and not updated TaxoBacGen althrough the construction process is similar : TaxoBacGen is an ACNUC format database where indications obtained through nomenclature control and type strain identification are added to GenBank informations fields.

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