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ClustScan (the Cluster Scanner) is an integrated suite of computer programs that take a "top down" approach to the annotation of gene clusters encoding Thiotemplate Modular Systems (TMS). It is a program package written in Java. ClustScan runs on a LINUX server with a Java client on the user's computer compatible with Windows, MacIntosh and Linux operating systems. ClustScan can analyse the large amounts of data produced by sequencing projects (genome and metagenome data sets) and can generate good predictions of the most likely chemical products from these gene clusters, allowing identification of interesting clusters. Rapid progress in sequencing technology makes the use of ClustScan even more important. Without such a tool, it is not practical to carry out sufficiently detailed analyses of the mass of data already available today. For example, even using a conservative estimate that every actinobacterial genome contains 10 TMS gene clusters and that 1.000 sequenced genomes will soon be available, there will be 10.000 new TMS gene clusters, potentially encoding novel chemical entities.