Island page
All islands predicted in chosen host are presented here.
The SVG visually displays the predicted islands as
on the circular graph.
Hovering on the pink island rectangle will indicate the position of the island in the genome.
The legend below the graph contains further explanation about what is being plotted together with a definition box on the SWGIS parameters.
This is followed by an information box on the chosen host which includes taxonomy and general information.
The NCBI link will take users to the NCBI nucleotide page of the host in a new window.
The islands list appears below the information box.
Islands with an asterisk (*) contain ribosomal proteins and may indicate a False Positive Prediction!
Start
This link will display all relevant information regarding the specific island. This includes genes, annotation, QuickGO ontology and BLASTP hits for genes.
Island text
This will display the SWGIS generated island GenBank file in the browser.
For a quick inspection of the file this option is preferable.
If you do need to work with and/or keep the file, the download option is suggested.
GRV_RV
GRV – Globally normalized relative variance of the oligonucleotide usage - host.
RV – Relative variance of the oligonucleotide usage - island.
Increase in the divergence between GRV and RV indicates horizontal transfer.
GRV_RV indicates this divergence by GRV/RV.
It is possible to search the database for similar GRV_RV ratio's with this tool.
The link opens with a collection of islands with a similar GRV_RV ratio to the island selected.
It is possible to decrease/increase this collection by setting limits on the ratio in the supplied limit boxes.
D
D – Distance between two oligonucleotide usage patterns, i.e local (island) and global (host).
It is possible to search the database for similar D values with this tool.
The link opens with a collection of islands with a similar D value to the island selected.
It is possible to decrease/increase this collection by setting limits on the ratio in the supplied limit boxes.
This value is also indicative of the age of a selected island.
The process of amelioration alters genomic fragments to resemble the host.
High value D islands are suggested to be more recently acquired.
Low values of D indicate a longer association with the host.
PS
PS – Pattern Skew, distance between the two patterns of the direct and reverse strands of the same DNA sequence
It is possible to search the database for similar PS values with this tool.
The link opens with a collection of islands with a similar PS value to the island selected.
It is possible to decrease/increase this collection by setting limits on the ratio in the supplied limit boxes.
Clusters
Non-overlapping, distinct clusters were identified by means of the Markov Clustering Algorithm (MCL).
OUP similarity between islands was used as a similarity measure in cluster creation.
Sub Clusters
Non-overlapping, distinct clusters were identified by means of the Markov Clustering Algorithm (MCL).
OUP similarity between islands was used as a similarity measure in cluster creation.
Large clusters were subjected to further clustering to obtain smaller sub clusters.
BLASTN
Sequence similarity hits between islands were identified by means of BLASTN.
E-value threshold was set at 10 ^ -6.
Key Word Confirmation
The presence of certain genes in an island further confirms the existence of the island in the host.
Islands containing these genes are marked with a plus in this column.
These gene annotations include transport, transposon, transposable element, transposase, integrase, is-element, phage and relaxase.
Other DB Confirmation
An island that is also present in another database will be indicated here.
Overlaps are searched for in both PAIDB and IslandViewer.
If an overlap is found it is possible to view the island contained in the other database.
Download Island
Any island of interest may be downloaded in a GenBank file format and saved.