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Old Warwick MLST Website

Important Information

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The website for the old MLST databases at the University of Warwick which was previously at http://mlst.warwick.ac.uk (and http://mlst.ucc.ie before that) has now been retired. This is because the old MLST website has been replaced with EnteroBase. While it was possible to maintain the old MLST website for a while for the benefit of users, the old website could not be maintained because it supported an obsolete technology. It is now also recommended to obtain whole genome sequences which are more accurate than ABI sequencing. During the lifespan of the legacy MLST website, one third of the new alleles we received which were based on ABI sequences represented sequencing errors rather than real sequence variations. Resolving these errors manually was time consuming. In addition, we don't know how many new STs were wrong, because novel combinations of known alleles can be due to mix-ups rather than recombination.

In order to improve the quality of the database, we now demand that all new allele/STs be defined by NGS short reads. If you upload short reads into http://enterobase.warwick.ac.uk/, we will assemble the short reads and report to you back their allele designations. On top of this, you get access to additional information by comparing your genomes with >100,000 existing genomes from all over the world. These genomes were either published in NCBI short read archive database, or have been uploaded by other users.

The average cost for NGS sequencing of a bacterial strain is also now cheaper than ABI sequencing. If you have difficulties in getting NGS sequencing done, we suggest you get in touch with http://microbesng.uk/, which gives you cheap access to NGS. If you still want to stay with ABI sequencing, you can download all the alleles from EnteroBase and build up your own local MLST database. Alternatively, you can try http://pubmlst.org/, which is an online tool for allele identifications (but will not give you new alleles).