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


Web Applications - tools that allow predictions of genomic islands through a web interface

  • IslandViewer - integrates three different methods: SIGI-HMM, IslandPath-DIMOB, IslandPick. Contains pre-computed results for all sequenced genomes and allows user submitted genomes.(More Information)
  • IslandPick - is an automated comparative genomics based method that is one of the methods integrated into IslandViewer. Also, users can choose to run manual comparisons with genomes of their choice. (More Information)
  • MobilomeFINDER - comparative genomics method that identifies only those GIs that have inserted into tRNA sequences. Contains a few pre-computed results, but does allow for genome submission.

Downloadable Software - tools that once installed locally, can be used to make predictions of genomic islands

Databases - websites with only pre-computed genomic islands

  • MOSAIC - contains predicted conserved and strain specific regions using whole genome alignments for a limited number of bacterial genomes.
  • Islander - is a database of GIs along with integration sites for a limited number of bacterial genomes.
  • PAI DB - is a database of pathogenicity islands that is based on homology and sequence composition bias for detection.

Other Useful Software - tools that can help aid in the analysis of genomic islands

  • Artemis - is a genome viewer and annotation tool that allows further analysis of genes within and surounding predicted GIs. GI predictions in IslandViewer can be loaded directly into Artemis using the provided GenBank files.
  • Mauve - is a whole genome alignment tool that allows inspection of conserved regions across related species. Alignments can be created using the GenBank files provided with IslandViewer.

External Gene Annotation Datasets- datasets used for additional annotation of genes

Other resources - previous tools for genomic island predictions

  • PAI IDA - uses a combination of G+C content, dinucleotide frequency and codon usage to predict the location of GIs.