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

By Keith A. Jolley, Man-Suen Chan, Martin C. J. Maiden. BMC Bioinformatics, 2004

533 citations recorded by the source corpus.

BackgroundMulti-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.ResultsThe 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.ConclusionDevelopment 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.

Subfields: Clinical Biochemistry, Endocrinology, Immunology

View Paper: https://www.semanticscholar.org/paper/85b34c07ec9fcf12d3f4ef318993440078d19d41

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Clinical Biochemistry

1. Frank Moller Aarestrup
2. Martin C. J. Maiden
3. Ole Lund
4. Keith A. Jolley

In Endocrinology

1. Keith A. Jolley
2. Martin C. J. Maiden

In Immunology

1. Martin C. J. Maiden
2. Keith A. Jolley
3. Ole Lund
4. Morten Nielsen
5. Massimo Andreatta
6. Bjoern Peters
7. Alessandro Sette

Citations in the corpus

• Multilocus Sequence Typing System for the Endosymbiont Wolbachia pipientis (2006, background): “The data are fully portable between laboratories and allow extensive comparative analyses (22).”
• Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria (2012, background): “The MLST allele sequences and ST profile tables are stored in curated databases hosted at different sites around the world (1, 14, 15).”
• Guidelines for the validation and application of typing methods for use in bacterial epidemiology. (2007, background): “, Phred/ Phrap) can assess DNA sequence quality of individual traces or of contigs [282], most curators believe that manual curation remains the reference standard (PulseNet and SalmGene are the best known representatives of this category).”
• Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates (2005, background): “It provides unambiguous and portable data that allow the implementation of multiuser international databases (17).”
• The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies (2016, background): “The transition towards an era of ‘genomic epidemiology’ will require linking of newly sequenced genomes with the isolates and traditional sub-typing data in databases such as PulseNet [27] and MLSTdb [28] in order to preserve relevant epidemiological information for public health investigations.”
• BIGSdb: Scalable analysis of bacterial genome variation at the population level (2010, methodology): “The current generation of sequence typing databases [13-15] have been highly successful at linking isolate provenance to sequence data, contributing significantly to the widespread adoption of MLST and antigen sequence typing.”