IslandViewer 4 | An integrated interface for computational identification and visualization of genomic islands
Genome Upload

IslandViewer will be unavailable for at least five days during the week of April 19, 2021 for major scheduled maintenance (transitioning to a new database and hardware). It will not be possible to submit new jobs for analysis during this period. This update will provide stability fixes, security improvements, and updates to some of the underlying software. Please note that BLAST has been updated in the new version of IslandPick and minor variations in the output from this tool should be expected as a result. When the update is complete, you will be able to access any existing accounts and previous jobs as usual, but will be required to refresh your API token if you wish to use the HTTP API. If you have any questions or concerns, please do not hesitate to contact us at We apologize for any inconvenience and thank you for your understanding as we implement this major upgrade.

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.


(this may take several minutes)

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:

     CDS   complement(4043..4849)
       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.