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Comparative Study
. 2004 Jul 1:5:86.
doi: 10.1186/1471-2105-5-86.

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

Keith A Jolley  1 , Man-Suen Chan, Martin C J Maiden
Affiliations
Comparative Study

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

Keith A Jolley et al. BMC Bioinformatics. .

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 customized 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.

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Figures

Figure 1
Figure 1
Screenshot: Isolate query. Isolate databases can be queried by searching against any field or combination of fields.
Figure 2
Figure 2
Screenshot: Isolate search by cited publication. A list of publications cited within isolate records can be displayed and a narrower search performed by searching for individual authors. All isolates described in a particular paper can be displayed by selecting the 'Display' button from this list.
Figure 3
Figure 3
Screenshot: Allele query. Allele comparison will identify known alleles or determine the nearest allele with the nucleotide differences shown. An alignment of the query sequence to the nearest allele will be offered if EMBOSS is installed.
Figure 4
Figure 4
Screenshot: Advanced breakdown. Following a database query, the displayed dataset can be analysed further, including breaking down one field against another and displaying frequencies of unique combinations of selected fields.
Figure 5
Figure 5
The distributed structure of the Neisseria MLST and related databases. The profiles database contains all the allele sequences and allelic profiles (sequence types) and can be queried via network connections or directly through the web. The PubMLST isolate database encourages general submissions and represents the known diversity of strains. The MLST 107 and Czech 1993 isolate databases are also available through the Neisseria MLST website and contain reference [1] and project [11, 12] sets of isolate data (see site for further details). These isolate databases also retrieve information from non-MLST databases including those for PorA and FetA antigen typing and PubMed. Other private isolate databases (not shown) also make use of the profiles database.
See this image and copyright information in PMC

References

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