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TSEMA: interactive prediction of protein pairings between interacting families
National Center for Biotechnology (CNB-CSIC) C/Darwin, 3 Cantoblanco, 28049 Madrid, Spain 1 National Bioinformatics Institute (INB), Barcelona Supercomputer Centre C/Jordi Girona, 29 08034 Barcelona, Spain 2 Department of Biochemistry and Molecular Biology, Biomolecular Structure and Modelling Unit, University College London London WC1E 6BT, UK
*To whom correspondence should be addressed. Tel: +34 915854669; Fax: +34 915854506; Email: pazos{at}cnb.uam.es
Received February 13, 2006. Revised March 1, 2006. Accepted March 9, 2006.
An entire family of methodologies for predicting protein interactions is based on the observed fact that families of interacting proteins tend to have similar phylogenetic trees due to co-evolution. One application of this concept is the prediction of the mapping between the members of two interacting protein families (which protein within one family interacts with which protein within the other). The idea is that the real mapping would be the one maximizing the similarity between the trees. Since the exhaustive exploration of all possible mappings is not feasible for large families, current approaches use heuristic techniques which do not ensure the best solution to be found. This is why it is important to check the results proposed by heuristic techniques and to manually explore other solutions. Here we present TSEMA, the server for efficient mapping assessment. This system calculates an initial mapping between two families of proteins based on a Monte Carlo approach and allows the user to interactively modify it based on performance figures and/or specific biological knowledge. All the explored mappings are graphically shown over a representation of the phylogenetic trees. The system is freely available at http://pdg.cnb.uam.es/TSEMA. Standalone versions of the software behind the interface are available upon request from the authors.