Resources

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

• SIGI-HMM - measures codon usage to identify possible GIs and is one of the methods integrated into IslandViewer. (More Information)
• IslandPath-DIMOB - measures dinucleotide bias to identify possible GIs and is one of the methods integrated into IslandViewer. (More Information)
• Alien Hunter/IVOM - uses variable order motifs to measure sequence bias and predict GIs.

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

• Virulence Factor Database (VFDB) - provides annotations of genes as virulence factors in major pathogen genomes (Chen et al., 2012).
• PATRIC - database of integrated virulence and resistance gene annotations, as well as a multitude of other data (e.g. pathways, transcriptomics data) for major pathogen genomes (Wattam et al., 2014).
• Victor's virulence factors - a database of manually curated virulence factors
• Comprehensive Antibiotic Resistance Database (CARD) - a collection of manually curated antibiotic resistance genes as well as a predictive tool (Resistance Gene Identifier) (Jia et al., 2017).
• Pathogen-associated genes - genes found to be only in the genomes of pathogenic species based on a set criteria (Ho Sui et al., 2009).

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.