High throughput method for discovery of gene clusters

A high throughput method for identifying a gene or gene cluster involved in the biosynthesis of a prokaryotic microbial secondary metabolite natural product comprising:

• a) preparing, from isolated genomic DNA, a random small insert library comprised of DNA fragments of the genomic DNA and a random large insert library comprised of DNA fragments of the genomic DNA, wherein said small insert library has inserts smaller than said large insert library;
• b) determining the DNA sequence of at least part of a plurality of the fragments in the small insert library to form a plurality of Gene Sequence Tags (GSTs);
• c) comparing, under computer control, the DNA sequence of the GSTs or the amino acid sequence encoded by the DNA sequence of the GSTs with sequences in a database containing genes, gene fragments, DNA or amino acid sequences known to be involved in the biosynthesis of microbial secondary metabolite natural products to identify a GST that has sequence homology, as evidenced by an E value of 10−5 or lower, to a gene, gene fragment, DNA or amino acid sequence known to be involved in the biosynthesis of microbial secondary metabolite natural products;
• and
• d) hybridizing a nucleic acid probe comprising a sequence generated using the sequence of said GST identified in (c) to said large insert library to identify a DNA fragment from the large insert library, which DNA fragment contains the GST and a gene or gene cluster involved in the biosynthesis of a prokaryotic microbial secondary metabolite natural product.