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

IslandViewer is a computational tool that integrates four different genomic island prediction methods: IslandPick, IslandPath-DIMOB, SIGI-HMM, and Islander. For more information about methods and analyses see here and in the FAQs.

Try our new user management interface available under LOGIN (optional), and submit here your custom genome to predict genomic islands using IslandPick, IslandPath-DIMOB, and SIGI-HMM.

Or browse the pre-computed genomic island predictions for publicly available genomes, including Islander predictions as well:


 
   Example, Example (incomplete genome)


News
 

2017/07/25 We are currently updating IslandViewer 4 to include all genomes newly available in RefSeq as pre-computed results. While this takes place, custom genome uploads have been momentarily disabled. Custom genome analyses should be again available within 24h. We apologize for the inconvenience and thank you for your patience.

2017/05/08 - The article describing the novel features of IslandViewer 4 has been published in Open Access in Nucleic Acids Research - doi: 10.1093/nar/gkx343.

2017/04/19 - IslandViewer 4 has officially been released. Login to check out the new user management interface to easily access previous results, and obtain credentials to use the HTTP API to submit many genomes and retrieve their results. Get expanded genomic island predictions using the latest IslandPath-DIMOB version in less time thanks to the integration of MASH for distance calculation. Browse interactively newly pre-computed predictions by SIGI-HMM, IslandPath-DIMOB, IslandPick and Islander in one of the 6587 publicly available genomes in a streamlined visualization that still highlights antimicrobial resistance genes, virulence factors and pathogen-associated genes. IslandViewer 3 remains available here and links to previous IslandViewer 3 results will be automatically redirected.

2017/01/01 - A new version of IslandViewer will soon be available: IslandViewer 4 will feature improved predictive capabilities for larger datasets while retaining its flexible visualization interface. For users wishing to finalize an analysis, IslandViewer 3 will remain available with an alternative url. Please check the latest news or subscribe to our mailing list to be notified of new releases.

2016/09/06 - IslandViewer 3 has been updated to include all 5306 complete genomes available in public databases as pre-computed results and as a reference for contig reordering.

2016/05/02 - A planned power outage took place at SFU on May 1st. IslandViewer website remained available, enabling users to browse pre-computed genomic island predictions. The submission of custom genomes was disabled until all computing nodes were available again.

2016/03/24 - The download of AMR and virulence genes from pre-computed results is now available. All links, including those pointing to other software, have been checked and updated. We are preparing the release of IslandViewer 4 that will include an improved IslandPath version enabling a much higher recall and precision in genomic island prediction. If you are interested in being notified when new IslandViewer versions are released, please subscribe to the new mailing list.

2016/01/21 - Small changes have been made to IslandViewer for improved clarity and better acknowledgement of past work. If you haven't already, check out the latest IslandViewer paper published last summer. Much more on improved visualization and genomic island predictions to come soon.

2015/12/08 - Service was disrupted to IslandViewer and the SFU emergency power supply on Tuesday, December 8 while planned repairs took place. We apologize for the inconvenience.

2015/04/20 - Islandviewer 3 is now out of beta, however if you still need to access older analysis using IslandViewer 2 we will keep it available here for the next few months.

2015/03/03 - IslandViewer 3 has officially been released and is available here. IslandViewer 3 includes a new interactive genome visualization tool, IslandPlot, and expanded virulence factor, antimicrobial resistance gene, and pathogen-associated gene annotations, as well as homologs of these genes in closely related genomes. Notably, incomplete genomes are accepted as input in IslandViewer 3, though we strongly urge users to use complete genomes whenever possible. The old IslandViewer website will still be available for users to download results for any previously analyzed custom genomes, but will eventually be replaced by IslandViewer 3. If you have any questions, comments, or issues with IslandViewer 3, please contact us.

2015/01/01 - Interactive IslandPlot visualizations are now available for circular and linear genomes views. In addition to this, more curated virulence and resistance gene annotations have been incorporated, as well as homologs of these genes as determined using the Resistance Gene Identifier (RGI) and a custom approach for virulence factors. An updated pathogen-associated genes analysis has also been complete for all available genomes.

2013/03/12 - Pathogen-associated gene annotations are now available on top of GI predictions, as determined in the study by Ho Sui et al., 2009. Custom genome submissions are back online, but if you are experiencing any difficulties, please don't hesitate to contact us. Note that this pathogen-associated genes analysis is currently being updated for a future data release Some genomes will not have any results until this update is completed.

2013/03/10 - Genome submissions are currently unavailable as we are upgrading our submission pipeline. Any jobs submitted on March 10th, 2013 may need to be re-run once the pipeline has been upgraded. We anticipate the pipeline should be back up within one or two days. Please don't hestitate to contact us if you have any further questions. Thank you for your patience as we improve IslandViewer!

2012/12/31 - New changes have been implemented in IslandViewer. This includes incorporation of virulence factor and antibiotic resistance gene classifications from the Virulence Factor Database (VFDB) (see Chen et al., 2012) and the Antibiotic Resistance Gene Database (ARDB) (see Liu et al., 2009) respectively, on top of GI predictions as well as a new side-by-side visualization page to compare two genomes. Please note that genomic island predictions have not changed.