Submission of data to the Bacteroides fragilis databases

All users are welcome to submit their strain information and new allele sequences to our databases. 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.

In order to maintain the quality of the data, the databases are curated and all submissions will be checked before entry.

Automated submission system

We have an automated system for submission of new alleles, profiles and isolate data. You can access this by clicking the 'Submissions' link in either the typing database (for alleles and allelic profiles) or the isolate database (for isolates with or without genomes). Note that any data submitted via the automated submission system will be public.

  • New allele sequences need to be trimmed to the start and end sites of the locus (see existing alleles for comparison). Sequences determined by whole genome methods can be submitted as FASTA files. Sequences determined by Sanger methods should be accompanied by a minimum of two high-quality sequence reads (ABI/SCF trace files), with at least one in each direction, which can be uploaded as supporting data. If you are submitting multiple alleles for the same locus then please put them in a single submission rather than multiple individual submissions - it takes much longer to curate, and you will likely hit a pending submission limit, if you send too many alleles as individual submissions.
  • New profile/ST assignment requires that you also submit data for an isolate that has that profile. Please add the isolate name to the id field of the profile submission and make a corresponding submission to the isolate database. To clarify - you need to make both a new profile submission to the sequence definition database and a separate, corresponding, submission to the isolate database (either an isolate or a genome submission - not both!). If your profile contains new alleles then you need to submit these for assignment first.
  • Isolate data templates in Excel format can be downloaded from the submission system.
  • Whole genome data can be submitted through the system. Please make a genome submission and attach contig files as supporting files. Contigs should be in a single FASTA file for each isolate. FASTA files may be either uncompressed (.fas, .fasta) or gzip/zip compressed (.fas.gz, Make either an 'isolate' submission or a 'genome' submission - not both.

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.

Access the submission system

  • Typing (allele and ST definitions)
  • Isolates (with or without associated genome assemblies)