2023-01-25 - Islandviewer was made available (and we notified those who wanted to be contacted) on January 16th. Thank you for your patience and our sincere apologies for the longer-than-expected down time. Over the past week we’ve been verifying a new update process can occur in the background and we now confirm this is reliably running. This update process, that adds new pre-computed genomes to Islandviewer, will still be ongoing in the background for approximately the next month, but users will be able to upload genomes to Islandviewer and run the Islandviewer pipeline in the meantime. We felt this “background update” was important to implement to reduce the amount of downtime needed for a major update. Once this has concluded, all new pre-computed genomes will become available and we will post notice of this. If you have any questions about this update process, or if you would like to be specifically notified when the update has completed, please contact us at firstname.lastname@example.org or join the mail list as noted under Contact us at http://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
Genomic island predictions can be calculated for your genome using IslandPick, IslandPath-DIMOB, and SIGI-HMM. More Information. See our FAQs
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.