Island page
All islands predicted in a chosen host are presented here.
The SVG visually displays the predicted islands as
on the graph.
The legend below the graph contains further explanation about what is being plotted together with a definition box on the SWGIS v2.0 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 against the Pre_GI database for all genes comprising the said island.
Island text
This will display the SWGIS v2.0 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.
D
D – Distance between two oligonucleotide usage patterns, i.e local (island) and global (host).
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.
BLASTN
Sequence similarity hits with islands in the Pre_GI database were identified by means of BLASTN
This was done to search for the possibility of bacterial-to-eukaryote horizontal gene transfers
E-value threshold was set at 10 ^ -1.
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, relaxase and t_RNA elements
Download Island
Any island of interest may be downloaded in a GenBank file format and saved.