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Submission of data

All users are welcome to submit their strain information and new allele sequences to our databases for Helicobacter pylori. This information will be made available on this web site.  In order that queries and requests for strains can be addressed to the submitter of isolate data, the name and affiliation of the submitter will be displayed on the website.  E-mail addresses are not displayed but can be requested from the curator.

Since almost every isolate of Helicobacter has new allele sequences at each locus, it is not practical to manually curate each new allele, which is the normal procedure for other MLST databases.

Please, therefore, send new allele sequences for assignments in FASTA format using the automated submission system.

Automated submission system

We have introduced an automated system for submission of new alleles, profiles and isolate data.

New allele sequences need to be trimmed to the start and end sites of the locus (see existing alleles for comparison).

Whole genome data can be submitted through the system. Please upload new isolate records and attach contig files as supporting files. Contigs should be in a single FASTA file for each isolate.

Users will need an account in order to use the submission system. Please register if you do not already have an account.

Please read the submission system documentation for further details.

Citing the database

The preferred format for citing this website in publications is:

This publication made use of the Helicobacter pylori Multi Locus Sequence Typing website (https://pubmlst.org/ helicobacter/) developed by Keith Jolley and sited at the University of Oxford (Jolley & Maiden 2010, BMC Bioinformatics, 11:595). The development of this site has been funded by the Wellcome Trust and European Union.

Status

Sequence database
Sequences: 19348
Profiles (MLST): 3143
Last updated: 2017-06-01

Isolate database
Isolates: 2225
Last updated: 2016-12-07