Institut Pasteur MLST Database Administration

Submission data document

To incorporate your profile and isolate information into the database, we require the following information :

  1. Please provide your full address, first and last name, and institution.

  2. For each new allele that does not already exist in the database, please send us at least two chromatogram traces (for example in .ab1 or .scf format). Ideally, each nucleotide over the length of the template should be supported by at least two traces without ambiguity. Please label your chromatogram trace files starting with the strain code (avoiding special characters such as space, dot,slash, etc), followed by underscore, followed by the gene name written exactly as in the database, followed by underscore, followed by any information you would like, followed by '.ab1' or '.scf'. Example: SB1_rpoB_398509385.ab1

  3. For each new profile that does not already exist in the database, we request that at least one reference strain be submitted to the isolates data base. The isolate information can be embargoed if you would like it to appear at a later stage, for example when a publication is accepted, but we request the info at the stage of profile coding. Note that we request the strain info, NOT the strain culture to be sent to us.

  4. Please use the enclosed Excel templates for profile and isolate data (home page) submission or refer to the existing isolates database to check the possible information for each field. Please note that the information for some fields may be required, while other is optional. IMPORTANT: please do not reorder or rename the columns.

  5. We encourage submission of all isolates of your studies, so that the database would be as representative of the natural populations as possible. Thus, please do not restrict yourself to submitting only isolates that represent new profiles.

    Please do not hesitate to contact us for further information. We would be grateful if you would acknowledge, in your publications, the efforts in the Acknowledgments section: 'We thank platform Genotyping of Pathogens and Public Health (Institut Pasteur) for coding MLST alleles and profiles.

PF8 Genotyping of Pathogens and Public Health Platform
25-28, Rue du Docteur Roux. 75724 Paris Cedex 15 . FRANCE
Tel + (33) 1 45 68 83 24 Fax + (33) 1 40 61 39 43
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Databases are maintained by Sylvain Brisse, Ghislaine GUIGON and Jean-michel THIBERGE using software developed by Keith Jolley at Oxford (Jolley et al. 2004, BMC Bioinformatics, 5:86). For any suggestion, please contact pf8-bioinfo

This site is hosted by the technological platform Genotyping of Pathogens and Public Health of Institut Pasteur.