SubtiList: a relational database for the Bacillus subtilis genome.

I Moszer; P Glaser; A Danchin

doi:10.1099/13500872-141-2-261

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SubtiList: a relational database for the Bacillus subtilis genome.

I Moszer·P Glaser·A Danchin

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Abstract

In the framework of the international collaborative project aiming to sequence the whole Bacillus subtilis chromosome, we have created a relational database for managing and analysing information associated with the molecular genetics of this bacterium: SubtiList. It allows recovery of non-redundant DNA sequences of the B. subtilis genome, as well as related information, i.e. genes, proteins, etc. A logical structure has been designed with appropriate links between the different objects, and a set of procedures has been implemented for data updating and management. The database is organized around a core constituted by all known contigs of B. subtilis, i.e. sets of non-redundant sequences created from original entries in the EMBL data library. A user-friendly interface has been developed to make the database easy to consult. Sequence analysis tools have been integrated into the database, such as a program for rapid similarity searching of protein data banks, and a powerful DNA pattern searching program. Thanks to the consistency of SubtiList, we have performed a codon usage analysis by Factorial Correspondence Analysis, and a study of the distribution of the isoelectric points of known proteins of B. subtilis. The SubtiList database is available through anonymous ftp (address 'ftp.pasteur.fr' or IP number 157.99.64.12, directory '/pub/GenomeDB/SubtiList').

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Algorithms Bacillus subtilis Bacterial Proteins DNA, Bacterial Databases, Factual Genetic Code Genome, Bacterial Isoelectric Point Logic Sequence Analysis, DNA Software Comparative Study Journal Article Research Support, Non-U.S. Gov't

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I Moszer, P Glaser, A Danchin. 1995. SubtiList: a relational database for the Bacillus subtilis genome.. https://doi.org/10.1099/13500872-141-2-261

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