Nucleic Acids Research Advance Access originally published online on October 31, 2008
Nucleic Acids Research 2008 36(21):6882-6892; doi:10.1093/nar/gkn685
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Nucleic Acids Research, 2008, Vol. 36, No. 21 6882-6892
© 2008 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.
Computational Biology |
ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures
1Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia, 2Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany, 3Novalis Ltd, Bo
idara Adije 17, 10000 Zagreb, Croatia and 4The School of Pharmacy, University of London, 29/39 Brunswick Square, London WC1N 1AX, UK
*To whom correspondence should be addressed. Tel: +385 1 4605013, Fax: +385 1 4836083; Email: dhranueli{at}pbf.hr
Received June 19, 2008. Revised September 23, 2008. Accepted September 24, 2008.
The program package ‘ClustScan’ (Cluster Scanner) is designed for rapid, semi-automatic, annotation of DNA sequences encoding modular biosynthetic enzymes including polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS) and hybrid (PKS/NRPS) enzymes. The program displays the predicted chemical structures of products as well as allowing export of the structures in a standard format for analyses with other programs. Recent advances in understanding of enzyme function are incorporated to make knowledge-based predictions about the stereochemistry of products. The program structure allows easy incorporation of additional knowledge about domain specificities and function. The results of analyses are presented to the user in a graphical interface, which also allows easy editing of the predictions to incorporate user experience. The versatility of this program package has been demonstrated by annotating biochemical pathways in microbial, invertebrate animal and metagenomic datasets. The speed and convenience of the package allows the annotation of all PKS and NRPS clusters in a complete Actinobacteria genome in 2–3 man hours. The open architecture of ClustScan allows easy integration with other programs, facilitating further analyses of results, which is useful for a broad range of researchers in the chemical and biological sciences.