Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data.
BACKGROUND
Modern comparative genomics does not restrict to sequence but involves the comparison of metabolic pathways or protein-protein interactions as well. Central in this approach is the concept of neighbourhood between entities (genes, proteins, chemical compounds). Therefore there is a growing need for new methods aiming at merging the connectivity information from different biological sources in order to infer functional coupling.


RESULTS
We present a generic approach to merge the information from two or more graphs representing biological data. The method is based on two concepts. The first one, the correspondence multigraph, precisely defines how correspondence is performed between the primary data-graphs. The second one, the common connected components, defines which property of the multigraph is searched for. Although this problem has already been informally stated in the past few years, we give here a formal and general statement together with an exact algorithm to solve it.


BACKGROUND
The algorithm presented in this paper has been implemented in C. Source code is freely available for download at: http://www.inrialpes.fr/helix/people/viari/cccpart.
Boyer
Frédéric
F
INRIA Rhône-Alpes, HELIX Group 655 avenue de l'Europe, 38334 Montbonnot Cedex, France.
Morgat
Anne
A
Labarre
Laurent
L
Pothier
Joël
J
Viari
Alain
A
D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016678:Genome; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D025941:Protein Interaction Mapping; D012335:RNA, Ribosomal / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry; D012984:Software
D012335:RNA, Ribosomal; D012343:RNA, Transfer