Inferring functional coupling of proteins using the Evolutionary Bond Energy Algorithm

In this paper, we propose a new method for inferring functional relationships between proteins from their phylogenetic profiles. The evolutionary bond energy algorithm (EBEA) enhances the greedy BEA clustering algorithm with genetic search. We conducted a series of experiments using phylogenetic profiles provided by the Cluster of Orthologous Groups of Proteins (COG) database. Experimental results demonstrate that the proposed method is capable of inferring meaningful clusters of functionally related proteins

[1]  Jacalyn M. Huband,et al.  bigVAT: Visual assessment of cluster tendency for large data sets , 2005, Pattern Recognit..

[2]  David E. Goldberg,et al.  Genetic Algorithms in Search Optimization and Machine Learning , 1988 .

[3]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[4]  D. Vitkup,et al.  Predicting genes for orphan metabolic activities using phylogenetic profiles , 2006, Genome Biology.

[5]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Paul J. Schweitzer,et al.  Problem Decomposition and Data Reorganization by a Clustering Technique , 1972, Oper. Res..

[7]  Simon Kasif,et al.  Identification of functional links between genes using phylogenetic profiles , 2003, Bioinform..

[8]  Julio Collado-Vides,et al.  A powerful non-homology method for the prediction of operons in prokaryotes , 2002, ISMB.

[9]  D. Eisenberg,et al.  Protein function in the post-genomic era , 2000, Nature.

[10]  E. Marcotte,et al.  Computational genetics: finding protein function by nonhomology methods. , 2000, Current opinion in structural biology.

[11]  J. Bezdek,et al.  VAT: a tool for visual assessment of (cluster) tendency , 2002, Proceedings of the 2002 International Joint Conference on Neural Networks. IJCNN'02 (Cat. No.02CH37290).

[12]  David S. Johnson,et al.  Computers and Intractability: A Guide to the Theory of NP-Completeness , 1978 .

[13]  Phipps Arabie,et al.  The bond energy algorithm revisited , 1990, IEEE Trans. Syst. Man Cybern..