TreeDet: Predicting Functional Residues in Protein Sequence Alignments

NOTE: We Strongly encourage users to create their alignments! (ClustalW, ProbCons, Muscle and T-COFFEE are available tools for this purpose). TreeDet IS NOT an alignment tool.

The TreeDet (Tree Determinant) Server is a system designed to integrate results from methods that predict functional sites in protein families. These methods take into account the relation between sequence conservation and evolutionary importance. TreeDet fully analyses the space of protein sequences in user-uploaded multiple sequence alignments. The methods implemented in the server represent three main classes of methods for the detection of family-dependent conserved positions, a tree-based method, a correlation based method and a method that employs a principal component analyses coupled to a cluster algorithm. An additional method is provided to highlight the reliability of the position in the alignments.

What's new in TreeDet from previous versions.

• - We do not support IE anymore.

• - Increased usability capabilities.

• - Now you can visualise results stored as xml from previous runs using the "Previous Results" application.

• - The original methods are still available. We have re-implemented the sequence space based method. The old FASS method has been replaced by the S3Det method (in the Help section the method is explained).