ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures

• Published in: Nucleic acids research Vol. 36; no. 21; pp. 6882 - 6892
• Main Authors: Starcevic, Antonio, Zucko, Jurica, Simunkovic, Jurica, Long, Paul F, Cullum, John, Hranueli, Daslav
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.12.2008; Oxford Publishing Limited (England)
• Subjects: Actinobacteria; Animals; Anti-Bacterial Agents - biosynthesis; Anti-Bacterial Agents - chemistry; biochemical pathways; Catalytic Domain; chemical structure; Computational Biology; Computer Graphics; data collection; DNA; Gene Order; Genomics; hybrids; invertebrates; ligases; metagenomics; Models, Molecular; multigene family; nucleotide sequences; Peptide Synthases - chemistry; Peptide Synthases - genetics; polyketide synthases; Polyketide Synthases - chemistry; Polyketide Synthases - genetics; prediction; Sequence Analysis, DNA; Software; stereochemistry; Systems Integration
• DOI: 10.1093/nar/gkn685
• ISSN: 0305-1048; 1362-4962

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.