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Nucleic Acids Research Advance Access originally published online on April 28, 2009
Nucleic Acids Research 2009 37(Web Server issue):W129-W134; doi:10.1093/nar/gkp264
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W129-W134
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

FMM: a web server for metabolic pathway reconstruction and comparative analysis

Chih-Hung Chou1, Wen-Chi Chang2,3, Chih-Min Chiu1, Chih-Chang Huang2 and Hsien-Da Huang2,3,*

1Institute of Molecular Medicine and Bioengineering, 2Institute of Bioinformatics and Systems Biology and 3Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan, Republic of China

*To whom correspondence should be addressed. Tel: +886 3 5712121. ext.: 56952; Fax: +886 3 5739320; Email: bryan{at}mail.nctu.edu.tw

Received February 18, 2009. Revised April 6, 2009. Accepted April 8, 2009.

Synthetic Biology, a multidisciplinary field, is growing rapidly. Improving the understanding of biological systems through mimicry and producing bio-orthogonal systems with new functions are two complementary pursuits in this field. A web server called FMM (From Metabolite to Metabolite) was developed for this purpose. FMM can reconstruct metabolic pathways form one metabolite to another metabolite among different species, based mainly on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and other integrated biological databases. Novel presentation for connecting different KEGG maps is newly provided. Both local and global graphical views of the metabolic pathways are designed. FMM has many applications in Synthetic Biology and Metabolic Engineering. For example, the reconstruction of metabolic pathways to produce valuable metabolites or secondary metabolites in bacteria or yeast is a promising strategy for drug production. FMM provides a highly effective way to elucidate the genes from which species should be cloned into those microorganisms based on FMM pathway comparative analysis. Consequently, FMM is an effective tool for applications in synthetic biology to produce both drugs and biofuels. This novel and innovative resource is now freely available at http://FMM.mbc.nctu.edu.tw/.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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