Shotgun sequencing

Shotgun sequencing is a technique used in genome sequencing to put fragments of sequenced DNA in the order they are found in the genome. Because DNA sequencing by the Sanger method (chain termination) can only be done on relatively short fragments of DNA (around 100-1000bp), the target DNA goes through several rounds of fragmentation with restriction enzymes, transformation into E. coli and then sequencing by chain-termination to produce multiple reads (the term used to describe sequenced DNA). Because the DNA is fragmented with different restriction enzymes and sequenced repeatedly, many reads overlap and overlapping reads can be processed by a computer which attempts to put them into a continuous sequence called a contig.

A problem with shotgun sequencing is the prevalence of repetitive DNA in eukaryotic genomes. Because the base composition of repetitive DNA is, by definition, indistinguishable from other repetitive regions, it is not possible for this technique to precisely locate such regions in the genome. The location of repeat DNA is thus resolved by using more traditional techniques, such as recombinant analysis.