Multiple Antibiotic Resistance Annotator

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.

MARA is an on-line application that 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

Getting Started

You can browse the MARA 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
  4. sequence is processed)
  5. Choose the type of DNA molecule (chromosome, plasmid) if known (optional)
  6. Enter species information if known (optional)
  7. Paste in your sequence or upload a FASTA file using the Browse button (up to 5MB per file)
  8. Click "Annotate" to start the annotation process
  9. The sequence will appear in your work area under "My sequences".
  10. You can annotate more sequences without waiting for the annotation to
  11. complete.
  12. With a free account you can annotate up to 20 sequences per day.

Premium Accounts

RAC and MARA are free resources providing a knowledge base for antibiotic resistance genes, including those in gene cassettes, and a free annotation service. In addition to the free service, premium accounts benefit from:

 

For more information, pricing and account activation, consult the Spokade Premium Account page.

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 MARA will be added to the MARA 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.

Premium accounts have the option to bypass the review process (signup here)

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.

Conditions of Use

By using MARA you confirm that you are using MARA for research and educational purposes only and in particular that you do not use it for clinical or commercial purposes. You also agree that any new resistance gene, gene cassette, mobile element or other genetic element identified in a sequence you submitted may be added to the MARA database according to the following process.

  1. The genetic element will be assigned a unique temporary name and you will be given its sequence and name.
  2. The genetic element will be added to the MARA database but will only appear in your own private area. It won't be seen by anyone browsing the database.
  3. You will inform MARA staff of any permanent names assigned to this genetic element by an accepted relevant body (such as NCBI, ISfinder) or proposed in the literature. We will then change the temporary name to the permanent one.
  4. When the element is mentioned in the literature, GenBank or other public resource, or if given written permission by you, the genetic element will be added to the public area, along with any GenBank accession number. It will then appear in the relevant list under "Browse lists" and will be included in the features used to annotate submitted sequences.

How to cite

Acknowledgements

Spokade owns and maintains MARA, RAC, Attacca and all associated software used in this system.

The Australian Institute of Health Innovation at Macquarie University hosts the application.

RAC was funded by an ANDS data capture project grant (ANDS#DC5F) and New South Wales Health Capacity Building and Infrastructure Grant.