Synonym
Definition
CLUSEAN, the CLUster SEquence ANalyzer, is a BioPerl-based software pipeline for the annotation of secondary metabolite biosynthetic gene clusters encoding the biosynthesis of molecules with, e.g., antibiotic or anticancer activities. CLUSEAN contains modules for automated homology search, protein domain identification, and, in case of modular polyketide synthases and non-ribosomal peptide synthetases-containing pathways, substrate prediction for the biosynthetic enzymes.
Introduction
A majority of antimicrobials used in human medicine to combat infectious diseases, e.g., tetracycline, penicillin, vancomycin, or erythromycin, many anticancer drugs, and other bioactive molecules, e.g., the immunosuppressant rapamycin, are derived from microbial secondary metabolites, also denoted as natural products. These compounds are mainly synthesized by bacteria and fungi. Traditionally, screening for such compounds is performed by isolating potential...
References
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, et al. The Pfam protein families database. Nucleic Acids Res. 2002;30(1):276–80.
Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. ACT: the artemis comparison tool. Bioinformatics. 2005;21(16):3422–3.
Eddy SR. HMMER: profile hidden Markov models for biological sequence analysis. 2001. Available from: http://hmmer.janelia.org/.
Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, et al. AntiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 2011;39(Web Server issue):W339–46.
Nguyen T, Ishida K, Jenke-Kodama H, Dittmann E, Gurgui C, Hochmuth T, et al. Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection. Nat Biotechnol. 2008;26(2):225–33.
Rausch C, Weber T, Kohlbacher O, Wohlleben W, Huson DH. Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). Nucleic Acids Res. 2005;33(18):5799–808.
Röttig M, Medema MH, Blin K, Weber T, Rausch C, Kohlbacher O. NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res. 2011;39(Web Server issue):W362–7
Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, et al. Artemis: sequence visualization and annotation. Bioinformatics. 2000;16(10):944–5.
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, et al. The Bioperl toolkit: perl modules for the life sciences. Genome Res. 2002;12(10):1611–8.
Weber T, Rausch C, Lopez P, Hoof I, Gaykova V, Huson DH, et al. CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. J Biotechnol. 2009;140(1–2):13–7.
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© 2013 Springer Science+Business Media New York
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Weber, T., Blin, K. (2013). CLUSEAN, Overview. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_706-4
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DOI: https://doi.org/10.1007/978-1-4614-6418-1_706-4
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