Galileo AMR allows

  1. Browsing of the repository of antibiotic resistance genes and selected mobile elements
  2. Annotation of resistance genes and associated mobile elements in bacterial DNA sequences
  3. Contribution of new resistance genes and mobile elements not yet in the database

Bacteria that cause infections are becoming increasingly resistant to antibiotics. In Gram-negative bacteria much of this resistance is caused by mobile resistance genes. Understanding the genetic elements responsible for spread of resistance genes is important for monitoring and predicting the spread of resistance in these organisms. We have developed a unique system (Attacca) that has allowed creation an archive of relevant elements and identification of these elements in bacterial DNA sequences. The aim of this project is to make our repository of antibiotic resistance genes available to the wider research community, to allow researchers to annotate sequences containing resistance genes and associated mobile elements using our system and to contribute new entries to the repository as these are found.

Getting Started

You can browse the Galileo AMR database (click on Browse lists) and once you have registered (click on Login, then register new user), you can annotate sequences using the Attacca engine (Tsafnat G, Coiera E, Partridge SR, Schaeffer J, Iredell JR. Context-driven discovery of gene cassettes in mobile integrons using a computational grammar. BMC Bioinformatics. 2009;10:281).

To annotate a sequence

  1. Select "Annotate new sequence" (login required)
  2. Enter a short description/name for the sequence you want to annotate (this is for your own use)
  3. Choose a sequence type from the drop down (this will affect how your sequence is processed)
  4. Choose the type of DNA molecule (chromosome, plasmid) if known (optional)
  5. Enter species information if known (optional)
  6. Paste in your sequence or upload a FASTA file using the Browse button (up to 5MB per file)
  7. Click "Annotate" to start the annotation process
  8. The sequence will appear in your work area under "My sequences".
  9. You can annotate more sequences without waiting for the annotation to complete.

Sequence Annotation

When a sequence is first submitted its status will be listed as "in progress". Annotation time will depend on the length of your sequence, the load on our system and whether a review is required or not. You can now close the browser and return to the "My sequences" page at a later time to check the status of your sequences.
Some sequences maybe automatically chosen for review. Example are sequences that contain gaps in cassette arrays that may be novel cassettes, sequences that contain gaps that may be novel IS, and sequences that contain potentially novel variants of resistance or other genes. The status of such sequences will be "under review" until we have completed the review.

Novel genes, gene cassettes, IS etc. that are discovered using Galileo AMR will be added to the Galileo AMR database.

If a resistance gene that is not in our database is identified during the review process then it will be added to your own private database and you will be contacted. Please refer to the Conditions of Use below.

An annotated sequence that does not require review will show the status as being "annotated".

When the annotation of the sequence is complete, it will say "annotated". Annotated sequences that you no longer require can be deleted by clicking on the "Delete" icon.

You will be able to see the annotation report by clicking on the "View" icon.

 

How to cite

When referring to cassettes annotated using this system please cite:
Partridge SR, Tsafnat G, Coiera E, Iredell JR. Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol Rev. 2009 Jul;33(4):757-84.

When referring to the annotation algorithm please cite:
Tsafnat G, Coiera E, Partridge SR, Schaeffer J, Iredell JR. Context-driven discovery of gene cassettes in mobile integrons using a computational grammar. BMC Bioinformatics. 2009;10:281