2022-05-24 - NOTE SCHEDULED DOWNTIME: IslandViewer and its web submission system will go down for scheduled maintenance for one week beginning Monday, May 30. We apologize for the inconvenience. If you would like to be notified when it is available again, please contact us at firstname.lastname@example.org or join the mail list as noted under Contact us at https://www.pathogenomics.sfu.ca/islandviewer/contactus/.
Users can now log in the new user management interface (see LOGIN menu) using Github, Google or Twitter credentials facilitating access to results.
To analyze larger batches of genomes, an HTTP API is available to submit genomes and retrieve results programmatically using curl, python or perl. More information is available here
We only accept user genomes that are formatted in EMBL or GENBANK format. Examples of genome files you should submit: GENBANK, EMBL. If your data was generated by Prokka, please ensure you use Prokkas --complaint flag to generate standard compliant output. IslandViewer will not be able to process it otherwise.
Note for incomplete genomes
Incomplete genomes are now accepted as input due to popular demand. However, whole genome analysis is still preferred to reduce false predictions and missing GIs. Please use at your own risk. We suggest to minimize the number of contigs before performing GI analysis and carefully evaluate all results from such custom jobs. Contigs will be ordered against a user-selected reference genome using the Mauve contig orderer (Rissman et al., 2009). Please note that annotation of the contigs is still required.
Hints for a successful analysis
Check and see if your genome file contains protein sequences for all CDSs AND the complete nucleotide sequence. A valid genome file should have full protein sequence data (under "\translation" tag within "CDS" primary tag) and nucleotide sequence data under ORIGIN or blank header in GENBANK or EMBL format, respectively. For example:
1 aaacaaacca aatatggatt ttattgtagc .......................
Please refer to the official GenBank documentation for more details.
Please also remove any lengthy comments from your files at this times These can create problems with downstream generation of the sequence files with genomic islands available for donwload.
If you are still having problems, see our FAQs.