clone contig sequencing method
clone contig sequencing methoda method to obtain the sequence of a GENOME involving the construction of a clone CONTIG map and sequencing the set of contiguous clones individually, by the shot-gun method. A library is constructed by cloning large (a few hundred kb to a few Mb), overlapping DNA inserts spanning the entire genome. These are usually generated by partial restriction (see PARTIAL DIGESTION of the genome, and cloned into large insert CLONING VECTORS, such as BACs, YACs or COSMIDS. The genomic inserts in the library of clones are assembled into clone contigs on the basis of overlap by, for example, CHROMOSOME WALKING or a clone fingerprinting technique, and then, ideally organized into a physical map of the genome. Individual genomic inserts are too large to be sequenced directly in a single reaction. A shot-gun sequencing approach can be used, in which each insert is sheared into a set of partially overlapping fragments, of sizes amenable to sequencing, and cloned. Each of these sub-clones is sequenced and the overlapping sequences assembled by computer into a contiguous sequence. The complete genome sequence can then be obtained by integrating the sequences for the individual clone inserts into the contiguous sequence.
The clone contig method is also referred to as hierarchical shot-gun sequencing or clone-by-clone approach. Compare WHOLE GENOME SHOT-GUN SEQUENCING.