engleski

ClustScan : an integrated program package for the detection and semi-automatic annotation of secondary metabolite clusters in genomic and metagenomic DNA data sets

Clustscan ("Cluster Scanner") is a semi-automatic DNA sequence analysis tool. It has a server-client architecture, with analysis being carried out on the server and a Java user interface for the client, which can be a PC, Mac or Linux machine. Using collapsible tree overviews and zoom functions, it is possible to work with whole genomes or large sets of metagenomic data. Using custom profiles it is possible to quickly identify secondary metabolite clusters. For modular biosynthetic clusters (polyketide synthases and non-ribosomal peptide synthetases), the cluster hierarchical architecture is represented by the program and allows prediction of product chemistry that can be exported in a standard chemical format (SMILES). The user can examine the basis of predictions made and override them if necessary. An open architecture allows easy extension of the scope of the program. The program package allows rapid scanning of large DNA data sets to identify interesting clusters of genes. This chapter reviews the subsequent development of a system published in 2008 [Starcevic et al., 2008] for the semi-automatic annotation of modular biosynthetic gene clusters from different sources, including metagenomes from free-living and symbiotic microorganisms and, in silico prediction of novel chemical structures.

polyketides, non-ribosomal peptides, Actinomycetes, metagenomes, genomes, gene clusters, annotation, generic programme package

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