|ThioFinder: identification of thiopeptide antibiotic gene clusters in DNA sequences|
Thiopeptides are sulfur-rich, highly modified heterocyclic peptides which are mainly active against Gram-positive bacteria including various drug-resistant pathogens [Bagley et al., Chem Rev, 2005]. Recently, it was discovered that many thiopeptides stop the proliferation of human cancer cells [Hegde, et al., Nat Chem, 2011]. Individual thiopeptides differ greatly in their biological activities and in their chemical structures, but the gene cluster organization is remarkably conserved [Yu, et al., ACS Chem Biol 2009; Liao, et al., Chem &Biol, 2009]. This stimulates the search for new thiopeptide gene clusters.
ThioFinder rapidly detects and graphically displays gene clusters involved in the biosynthesis of thiopeptide antibiotics utilizing a profile Hidden Markov Model approach. ThioFinder also contains a new classification of thiopeptide gene clusters, facilitates multiple sequence alignments of known proteins and newly identified homologues involved in thiopeptide synthesis, and it automates primer design for PCR amplification. ThioFinder is fully supported by the open-access, manually curated database ThioBase which contains genetic, chemical, and biological information from all known thiopeptides. New thiopeptide gene clusters can be submitted here for inclusion in ThioBase.
Reference: J. Li¶, X. Qu¶, X. He, L. Duan, G. Wu, D. Bi, Z. Deng, W. Liu*, H.Y. Ou* (2012) ThioFinder: a web-based tool for the identification of thiopeptide gene clusters in DNA sequences. PloS ONE, 7, e45878. (¶ These authors contributed equally to this work.) [Abstract]