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Publication    
PloS ONE, 2012, 7, e45878.

ThioFinder: a web-based tool for the identification of thiopeptide gene clusters in DNA sequences

J. Li, X. Qu, X. He, L. Duan, G. Wu, D. Bi, Z. Deng, W. Liu*, H.Y. Ou*

 Link to PubMed
 
Thiopeptides are a growing class of sulfur-rich, highly modified heterocyclic peptides that are mainly active against Gram-positive bacteria including various drug-resistant pathogens. Recent studies also reveal that many thiopeptides inhibit the proliferation of human cancer cells, further expanding their application potentials for clinical use. Thiopeptide biosynthesis shares a common paradigm, featuring a ribosomally synthesized precursor peptide and conserved posttranslational modifications, to afford a characteristic core system, but differs in tailoring to furnish individual members. Identification of new thiopeptide gene clusters, by taking advantage of increasing information of DNA sequences from bacteria, may facilitate new thiopeptide discovery and enrichment of the unique biosynthetic elements to produce novel drug leads by applying the principle of combinatorial biosynthesis. In this study, we have developed a web-based tool ThioFinder to rapidly identify thiopeptide biosynthetic gene cluster from DNA sequence using a profile Hidden Markov Model approach. Fifty-four new putative thiopeptide biosynthetic gene clusters were found in the sequenced bacterial genomes of previously unknown producing microorganisms. ThioFinder is fully supported by an open-access database ThioBase, which contains the sufficient information of the 99 known thiopeptides regarding the chemical structure, biological activity, producing organism, and biosynthetic gene (cluster) along with the associated genome if available. The ThioFinder website offers researchers a unique resource and great flexibility for sequence analysis of thiopeptide biosynthetic gene clusters. ThioFinder is freely available at http://db-mml.sjtu.edu.cn/ThioFinder/.


News in Chinese
硫肽生物合成基因簇的预测工具ThioFinder对外服务

硫肽 (Thiopeptides)是一类被高度修饰的、富含硫的微生物源环肽类化合物,对革兰氏阳性病原菌有很强抑制作用。近期还发现其对人癌细胞的增殖有明显抑制作用。其成员都具有一个以六元杂环为核心、由多个五元杂环和脱水氨基酸组成的典型环肽结构。最近,我组和中科院有机所刘文教授课题组合作,成功开发了产硫肽微生物挖掘服务器ThioFinder。它采用隐马尔科夫模型来表征已知硫肽合成关键酶的序列保守性,在高性能四路服务器上实现了新硫肽基因簇的准确和快速识别。此外,内置的开放知识库ThioBase收录了目前已知99个硫肽化合物的化学结构、生物活性、产生菌和合成基因簇等重要数据。这一服务器的建立和对外开放将有助于实现产硫肽微生物资源挖掘,进而应用组合生物合成方法开发出新的临床抗菌素。
 


 

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