Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks |
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Authors: | S June Oh Je-Gun Joung Jeong-Ho Chang and Byoung-Tak Zhang |
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Institution: | (1) Department of Pharmacology, Inje University College of Medicine, Busan, 614-735, Korea;(2) Center for Bioinformation Technology, Seoul National University, Seoul, 151-742, Korea;(3) Graduate Program in Bioinformatics, Seoul National University, Seoul, 151-742, Korea;(4) Biointelligence Laboratory, School of Computer Sci. and Eng., Seoul National University, Seoul, 151-742, Korea |
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Abstract: | Background To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor
as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional
phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms.
In contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional relationships
under different physiological conditions. However, evaluating the similarities or differences between metabolic networks is
a computationally challenging problem, and systematic methods of doing this are desirable. Here we introduce a graph-kernel
method for computing the similarity between metabolic networks in polynomial time, and use it to profile metabolic pathways
and to construct phylogenetic trees. |
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