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

We would appreciate researchers acknowledge IslandViewer and any datasets that they have used.

If you use IslandViewer for your research, please cite the most recent publication. Thank You!
Bertelli, C. et al. 2017.
"IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets"
Nucleic Acids Research. 2017 May 2.
doi: 10.1093/nar/gkx343

If you would like to do more comparative analysis of genomes/genomic islands try our new tool
IslandCompare
 

Download

GI Datasets

All predicted GIs can be downloaded for the following tools:

  1. IslandViewer (all methods)- (Excel, TAB, CSV)
  2. IslandPick - (Excel, TAB, CSV)
  3. IslandPath-DIMOB - (Excel, TAB, CSV)
  4. SIGI-HMM - (Excel, TAB, CSV)
  5. The Islander prediction database can be downloaded here. Islander predictions available in IslandViewer - (Excel, TAB, CSV)

The original positive and negative GI datasets for 118 bacterial chromosomes (in Langille et al., 2008) may be used for evaluating sequence composition based GI predictors.

An updated positive and negative reference dataset integrating IslandPick predictions from IslandViewer 3 and IslandViewer 4 in 104 bacterial genomes is available in tabular format and fasta format for evaluating sequence composition based GI predictors.

Source Code

Please note that the following three methods are integrated into IslandViewer: IslandPick, IslandPath-DIMOB and SIGI-HMM. Moreover, Islander predictions are available for some pre-computed genomes.

  1. IslandPick is currently very dependent on an in-house MySQL database of all published genomes, and is optimized for use on our computer cluster. Although it would require a significant amount of effort for a casual user to install, we still believe in open access to our software. Therefore, those researchers with sophisticated bioinformatics backgrounds are welcome to view and use our source code, which is available under a GPL license here.
  2. IslandPath-DIMOB source code is available under a GPL license here or in the Brinkman lab github. IslandPath-DIMOB requires that Perl, BioPerl, and other perl libraries and HMMER be installed on the user's computer.
  3. SIGI-HMM is available for download here.
  4. Islander is available for download here.

We would encourage users to contact us with any special requests or concerns.