mlstdbNet – distributed multi-locus sequence typing (MLST) databases

Keith A Jolley¹ , Man-Suen Chan² and Martin CJ Maiden¹

¹The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK

²Department of Paediatrics, Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK

author email corresponding author email

BMC Bioinformatics 2004, 5:86doi:10.1186/1471-2105-5-86


Published:	1 July 2004

Abstract

Background

Multi-locus sequence typing (MLST) is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments. The mlstdbNet software enables the implementation of distributed web-accessible MLST databases that can be linked widely over the Internet.

Results

The software enables multiple isolate databases to query a single profiles database that contains allelic profile and sequence definitions. This separation enables isolate databases to be established by individual laboratories, each customised to the needs of the particular project and with appropriate access restrictions, while maintaining the benefits of a single definitive source of profile and sequence information. Databases are described by an XML file that is parsed by a Perl CGI script. The software offers a large number of ways to query the databases and to further break down and export the results generated. Additional features can be enabled by installing third-party (freely available) tools.

Conclusion

Development of a distributed structure for MLST databases offers scalability and flexibility, allowing participating centres to maintain ownership of their own data, without introducing duplication and data integrity issues.