Fragment analysis is a general term used to describe genetic marker analysis experiments which rely on detection of changes in the length of a specific DNA sequence to indicate the presence or absence of a genetic marker. Marker analysis is a general genetic technique in which the sequence of the gene is not directly analyzed, but the presence of a particular allele or mutant version of the allele of the gene is inferred from the presence or absence of a linked DNA sequence which can serve as a marker for the allele. Genetic markers are usually polymorphic genetic sequences contained in or near an allele of interest, such as microsatellite or RFLPs, which allow the chromosomal alleles to be distinguished. Using a marker analysis approach, inheritance patterns within a family can be traced and a mutant allele associated with a disease can be identified by comparing the alleles of affected and unaffected individuals. Also, inheritance patterns in populations of humans, animals, plants, etc., can also be traced, making genetic marker analysis quite useful in population biology and ecology studies.
Marker analysis would be used instead of direct examination of a gene sequence for several reasons: A gene location may be known, but the gene sequence has not yet been determined and thus direct sequence comparison is not possible. If markers exist close to the gene locus, then the presence of mutant versions of the gene can be inferred through marker analysis. Marker analysis is much faster then direct gene sequencing. This is very helpful in population studies where the number of analyses needed can be very large.