| Date |
April 7, 2008 |
| Speaker |
Dr. Yukako Tohsato, Department of Bioscience and Bioinformatics, College of Information Science and Engineering, Ritsumeikan University |
| Title |
Metabolic Pathway Alignment Based on Compound Similarity |
| Abstract |
In many of the chemical reactions in living cells, enzymes act
as catalysts in the conversion of certain compounds into other
compounds. The pathway of a reaction is generally called the "metabolic
pathway," which is often abbreviated simply to "pathway." Comparative
analyses of the pathways formed by such reactions give important
information on their evolution and on pharmacological targets (Galperin
et al., 1998). I especially focused on "pathway duplication," which is
one of the hypotheses explaining the evolution of the metabolic
pathways. Pathway duplication suggests that evolution has occurred
through duplication of the genes encoding proteins within a pathway
(Schmidt et al., 2003). To analysis of pathway duplication, I have
developed some methods (Tohsato et al, 2003 and Tohsato et al, 2007).
One of the methods is a scoring system to express the degree of
similarity between reactions based on their compounds similarity. In the
method, I introduce the scoring system to the local alignment algorithm
based on dynamic programming to align between two pathways. I propose a
Z-score of the alignment score for metabolic pathway alignment. The
effectiveness of the method is demonstrated by applying the method to
pathway analysis of metabolic pathways in Escherichia coli. By their
results, I have found compound similarity between the purine metabolism
and the pyrimidine metabolism.
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