Paper Info
Title
CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways.
Abstract
Motivation: Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism. Results: We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms.
Year
DOI
Venue
2013
10.1093/bioinformatics/btt235
BIOINFORMATICS
Keywords
Field
DocType
algorithms,metabolic engineering
Data mining,Computer science,Source code,Theoretical computer science,Heuristics,Bioinformatics,Executable,Scripting language,Binary number
Journal
Volume
Issue
ISSN
29
13
1367-4803
Citations 
PageRank 
References 
5
0.47
22
Authors
3
Name
Order
Citations
PageRank
Gamze Abaka150.47
Türker Bíyíkoglu2887.40
Cesim Erten324916.76