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MLST.net / Multi Locus Sequence Typing Network
A nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet. The aim of MLST is to provide a portable, accurate, and highly discriminating typing system that can be used for most bacteria and some other organisms. It is envisaged that this approach will be particularly helpful for the typing of bacterial pathogens. To achieve this aim we have taken the proven concepts of multilocus enzyme electrophoresis (MLEE) and have adapted them so that alleles at each locus are defined directly, by nucleotide sequencing, rather than indirectly from the electrophoretic mobility of their gene products.
AgdbNet / Antigen sequence database
An antigen sequence database software for web-based bacterial typing. AgdbNet facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. The software is currently in use on at least five public databases for the typing of Neisseria meningitidis, Campylobacter jejuni and Streptococcus equi and can be set up to query internal isolate tables or suitably-configured external isolate databases, such as those used for multilocus sequence typing.
Kudoa septempunctata MLST Databases
A genotype database of Kudoa septempunctata. We have developed an intraspecific genotyping method, using the sequence variation of mitochondrial genes. We collected olive flounder samples from foodborne disease outbreaks, domestic fish farms or quarantine offices and investigated whether K. septempunctata genotype is associated with pathogenicity or geographic origin. The 104 samples were classified into three genotypes, ST1, ST2 and ST3. Frequency of symptomatic cases differed by genotypes, but the association was not statistically significant. Whereas K. septempunctata detected from aquaculture-raised and natural fish from Japan were either ST1 or ST2, those from fish inspected at quarantine from Korea to Japan were ST3. Our method can be applied to phylogeographic analysis of K. septempunctata and contribute to containing the foodborne disease.
HyperCAT
Provides access to three typing databases about the Bacillus cereus. HyperCAT incorporates analysis tools combining genotyping data from multiple MultiLocus Sequence Typing (MLST) schemes, as provided in the SuperCAT database, but also from the altogether different approaches Amplified Fragment Length Polymorphism (AFLP) and MultiLocus Enzyme Electrophoresis (MLEE). The database also contains pages presenting various statistics relating to strain distribution, data content and overlap, as well as descriptions of the supertree and supercluster building procedures.
PubMLST / Public MultiLocus Sequence Typing
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Hosts multi-locus sequence typing (MLST) data. PubMLST resources are hosted using the Bacterial Isolate Genome Sequence Database (BIGSdb) platform. A RESTful application programming interface (API) makes the curated and structured data on PubMLST accessible for programmatic access. Users may need to authenticate themselves, for instance to submit data for curation. Access to specific data resources can also be limited to registered users or project members.
BacWGSTdb
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A bacterial whole genome sequence typing database which is designed for clinicians, clinical microbiologists and hospital epidemiologists. BacWGSTdb borrows the population structure from the current multi-locus sequence typing (MLST) scheme and adopts a hierarchical data structure: species, clonal complex and isolates. When users upload the pre-assembled genome sequences to BacWGSTdb, it offers the functionality of bacterial genotyping at both traditional MLST and whole-genome levels. More importantly, users are told which isolates in the public database are phylogenetically close to the query isolate, along with their clinical information such as host, isolation source, disease, collection time and geographical location. In this way, BacWGSTdb offers a rapid and convenient platform for worldwide users to address a variety of clinical microbiological issues such as source tracking bacterial pathogens.
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