DOTA: A Simple Protein DOmain TAndem Repeat Analyzer

 

Input the domain sequences alignment (FASTA format)

           



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 This is an unpublished algorithm and is for demonstration purpose only.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.

Web server maintained by
© Minli Xu (minli@cmu.edu) 2010,2012

Last update: 26-June-2012 21:58 PM