MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites

BMC Bioinformatics

Proceedings

Masaaki Kotera¹  Toshiaki Tokimatsu¹  Susumu Goto¹  Minoru Kanehisa² 

[1] Bioinformatics Center, Institute for Chemical Research, Kyoto University, 611-0011, Uji, Kyoto, Japan;Bioinformatics Center, Institute for Chemical Research, Kyoto University, 611-0011, Uji, Kyoto, Japan;Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan;

关键词: Pairwise Alignment;    Alignment Method;    Short Path Length;    Atom String;    Maximum Common Subgraph;   

DOI  :  10.1186/1471-2105-12-S14-S1

来源: Springer

【 摘 要 】

BackgroundIn contrast to the increasing number of the successful genome projects, there still remain many orphan metabolites for which their synthesis processes are unknown. Metabolites, including these orphan metabolites, can be classified into groups that share the same core substructures, originated from the same biosynthetic pathways. It is known that many metabolites are synthesized by adding up building blocks to existing metabolites. Therefore, it is proposed that, for any given group of metabolites, finding the core substructure and the branched substructures can help predict their biosynthetic pathway. There already have been many reports on the multiple graph alignment techniques to find the conserved chemical substructures in relatively small molecules. However, they are optimized for ligand binding and are not suitable for metabolomic studies.ResultsWe developed an efficient multiple graph alignment method named as MUCHA (Multiple Chemical Alignment), specialized for finding metabolic building blocks. This method showed the strength in finding metabolic building blocks with preserving the relative positions among the substructures, which is not achieved by simply applying the frequent graph mining techniques. Compared with the combined pairwise alignments, this proposed MUCHA method generally reduced computational costs with improving the quality of the alignment.ConclusionsMUCHA successfully find building blocks of secondary metabolites, and has a potential to complement to other existing methods to reconstruct metabolic networks using reaction patterns.

【 授权许可】

Unknown   
© Kotera et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.