Frequently Asked Questions FAQ

Answer

Use of this form is free for academic purposes. For all other uses, please contact the authors.

Answer

Browsing the TYGS web page is free and does not require registration.

For submitting a TYGS job, an e-mail address has to be provided along with some genome sequences and/or GenBank accession IDs, the subject of the subsequent analysis. The e-mail address is the only piece of person-related information stored by the TYGS. All data associated with a TYGS job, including the e-mail address, are deleted after the job has finished and an additional amount of time has passed. The exact time of deletion is indicated in the notification e-mail and in the information badges in the top-right corner of the TYGS result page.

Additional information is found in the general privacy statement of the Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, in accordance with the General Data Protection Regulation.

Answer

Please see the GGDC/VICTOR FAQ for detailed instructions on how to specify accession numbers.

Answer

Please see the GGDC/VICTOR FAQ for detailed explanations of why an e-mail may get lost. Also note that the TYGS results are additionally displayed on a website.

Answer

While the TYGS database attempts to be as comprehensive as possible, a specific type-strain genome may be missing for a variety of reasons:

  • The genome has not yet been sequenced.
  • The genome sequence has been obtained but not been deposited in public databases.
  • The genome sequence has been deposited in public databases but cannot be identified because its metadata lack crucial information.
  • The genome sequence has been deposited in public databases but cannot be identified because a deposit of the type strain was used that is unknown to the TYGS database.
  • The genome sequence can be identified in public databases but fails the TYGS quality checks.

If you are aware of a type-strain genome sequence that is missing in the TYGS database, please contact the maintainers and provide information on this genome sequence as indicated above.

Prior to sending a report on a missing type-strain genome sequence, make sure the species or subspecies is not contained in the list for manual genome selection. If it is contained, you may better file a report on a type-strain genome sequence that is contained but not automatically found.

Answer

Click on the refresh symbol close to "Click to load or refresh tree (page needs to be viewed in https session)" on the tree page.

Answer

In addition to the routine import of taxonomic and genomic information, the following user-visible changes were applied to the database after the initial Nature Communications publication:

2019-07-23
Type(-strain) reference genome sequences with >500 contigs are accepted if the annotation contains a 16S rRNA gene sequence. When introduced this change resulted in the addition of only few dozens of new genome sequences.