title: SubtiList: a relational database for the Bacillus subtilis genome.
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').
authors.affiliation: Unité de Régulation de l'Expression Génétique, Institut Pasteur, Paris, France.
authors.forename: I
authors.initials: I
authors.lastname: Moszer
authors.forename: P
authors.initials: P
authors.lastname: Glaser
authors.forename: A
authors.initials: A
authors.lastname: Danchin
mesh_terms: D000465:Algorithms; D001412:Bacillus subtilis / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D016208:Databases, Factual; D005815:Genetic Code; D016680:Genome, Bacterial; D007526:Isoelectric Point; D008128:Logic; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial