A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise

Background: Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. Results: We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction usi...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Olivier Bastien, Philippe Ortet, Sylvaine Roy, Eric Maréchal
• Keywords: BMCBI 2005, CSHP, Homologous Proteins, Sequence Alignments