A MARKER is any sequence or locus which can be uniquely assigned to a position within a larger sequence, chromosome or genome.

Such markers are used as features to define a map of the region, in order that finer structural analysis can be performed, or function investigated.

In the context of HAPPY mapping, a marker is a short DNA sequence, usually derived from an STS, sequence read or clone-end or contig-end sequence, which can be amplified uniquely by PCR.

Each HAPPY marker can be defined by the forward and reverse PCR primer pair which amplifies it.