title: MP-Align: alignment of metabolic pathways.
abstract: BACKGROUND
  Comparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathways have been introduced in the literature as a first attempt in this direction. The approaches are based on some simplified representation of metabolic pathways and on a related definition of a similarity score (or distance measure) between two pathways. More recent comparative research focuses on alignment techniques that can identify similar parts between pathways.
  
  
  RESULTS
  We propose a methodology for the pairwise comparison and alignment of metabolic pathways that aims at providing the largest conserved substructure of the pathways under consideration. The proposed methodology has been implemented in a tool called MP-Align, which has been used to perform several validation tests. The results showed that our similarity score makes it possible to discriminate between different domains and to reconstruct a meaningful phylogeny from metabolic data. The results further demonstrate that our alignment algorithm correctly identifies subpathways sharing a common biological function.
  
  
  CONCLUSIONS
  The results of the validation tests performed with MP-Align are encouraging. A comparison with another proposal in the literature showed that our alignment algorithm is particularly well-suited to finding the largest conserved subpathway of the pathways under examination.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Alberich
authors.affiliation: Department of Mathematics and Computer Science, University of the Balearic Islands, Ctra, Valldemossa km, 7,5, E-07122 Mallorca, Spain. merce.llabres@uib.es.
authors.forename: Mercè
authors.initials: M
authors.lastname: Llabrés
authors.forename: David
authors.initials: D
authors.lastname: Sánchez
authors.forename: Marta
authors.initials: M
authors.lastname: Simeoni
authors.forename: Marc
authors.initials: M
authors.lastname: Tuduri
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D006019:Glycolysis; D053858:Metabolic Networks and Pathways; D015203:Reproducibility of Results; D013045:Species Specificity