SEQWORD Parameters
Enter values in the limit boxes provided to change range of parameter values retrieved.
Islands retrieved by default / chosen range are viewable by means of the hyperlink in the Island column.
Compositional and sequence similarity for islands within the range are availabe by means of the Neighbours and BLASTN links.
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.