Chromosome walking is a method in genetics for identifying and sequencing long parts of a DNA strand, e.g., a chromosome. As the traditional chain termination method does not allow long DNA strands to be sequenced, this method works by dividing the long sequence into several consecutive short ones.
The basic technique is as follows:
- A primer that matches the beginning of the DNA to sequence is used to synthesize a short DNA strand complementary to the unknown sequence, starting with the primer (see PCR).
- The new short DNA strand is sequenced using the chain termination method.
- The end of the sequenced strand is used as a primer for the next part of the long DNA sequence.
That way, the short part of the long DNA that is sequenced keeps "walking" along the sequence. The method can be used to sequence entire chromosomes (thus, chromosome walking). A different method with the same purpose which becomes more popular for large-scale sequencing (e.g., the Human Genome Project) is shotgun sequencing.
- Shotgun sequencing - an alternative method, using random, rather than consecutive, sub-strands.