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Open Access Software

ASMPKS: an analysis system for modular polyketide synthases

Hongseok Tae12, Eun-Bae Kong2 and Kiejung Park1*

Author Affiliations

1 Information Technology Institute, SmallSoft Co., Ltd., Jang-Dong 59-5, Yusung-Gu, Daejeon 305-343, South Korea

2 Deptartment of Computer Engineering, Chungnam National University, 220 Gung-dong, Daejeon 305-764, South Korea

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BMC Bioinformatics 2007, 8:327  doi:10.1186/1471-2105-8-327

Published: 3 September 2007

Abstract

Background

Polyketides are secondary metabolites of microorganisms with diverse biological activities, including pharmacological functions such as antibiotic, antitumor and agrochemical properties. Polyketides are synthesized by serialized reactions of a set of enzymes called polyketide synthase(PKS)s, which coordinate the elongation of carbon skeletons by the stepwise condensation of short carbon precursors. Due to their importance as drugs, the volume of data on polyketides is rapidly increasing and creating a need for computational analysis methods for efficient polyketide research. Moreover, the increasing use of genetic engineering to research new kinds of polyketides requires genome wide analysis.

Results

We describe a system named ASMPKS (Analysis System for Modular Polyketide Synthesis) for computational analysis of PKSs against genome sequences. It also provides overall management of information on modular PKS, including polyketide database construction, new PKS assembly, and chain visualization. ASMPKS operates on a web interface to construct the database and to analyze PKSs, allowing polyketide researchers to add their data to this database and to use it easily. In addition, the ASMPKS can predict functional modules for a protein sequence submitted by users, estimate the chemical composition of a polyketide synthesized from the modules, and display the carbon chain structure on the web interface.

Conclusion

ASMPKS has powerful computation features to aid modular PKS research. As various factors, such as starter units and post-processing, are related to polyketide biosynthesis, ASMPKS will be improved through further development for study of the factors.