TreeDet: Predicting Functional Residues in Protein Sequence Alignments

NOTE: NEW: A new stand-alone multiplatform application called Jdet (Muth et al. (2012). Bioinformatics 28 (4): 584-58) is now available (JDet). Jdet allows running S3det (Rausell et al. (2010) PNAS. 107(5)1995-2000) and Xdet (Pazos et al. (2006) Bioinformatics. 22(12):1440-1448) and provides an advanced platform for visualizing their results in a more flexible way.

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 The old FASS method has been replaced by the S3Det method (in the Help section the method is explained).

Technical support:, Scientific support:

PMID: 16844971 [PubMed - indexed for MEDLINE]