This web interface is to demonstrate the DOTA algorithm,
which I developed as a rotation project back in may 2010.
This web server is written in PHP and executes the original PERL scripts that I wrote two years ago.
DOTA can trace the domain evolution for proteins with tandem domain repeats.
The tracing result will be displayed in form of a tree-like structure.
This is an unpublished algorithm and is for demonstration purpose only. Please use with cautions.
The server will first calculate a pair-wise distance matrix based on the input fasta-format multiple sequence alignment.
Then an ALC (average-linkage clustering) like clutering algorithm will be used to trace the tandem domain repeats evolution history.
In the output, a tree-like structure (similar to a phylogeny) will illustrate how the domain evolved. The tree is actually a network with layers,
lines between horizontal layers indicate Tandem Domain Duplication (TDD) events.
Only Duplication event will be considered when inferring the history. Domain loss and transfer/shuffling events will not be inferred in the current framework. Please come back in future for updates.
For a description of the algorithm, or a running script, pleae contact the author.