There are basically two types of maps, genetic maps and physical maps, which differ in the methods used to construct them and in the metric that is used to measure the distance between genes.

Genetic maps

are constructed by determining how frequently two "markers", such as a physical trait, a particular medical syndrome, or a detectable DNA sequence, are inherited together. Two markers are one centimorgan apart if they are separated during transmission from parents to children one percent of the time. A centimorgan corresponds to a highly variable physical distance , the genome-wide average is believed to be roughly one million base pairs. There are many types of DNA markers to detect genetic variation among individuals. such as restriction fragment length polymorphisms ( RFLPs) and those markers from subtle variation in DNA sequence detect by denaturing gradient gel electrophoresis. Genetic maps have many uses, including identification of the genes associated with genetic diseases and other biological properties. Genetic maps also form an essential backbone or scaffold that is needed to guide a physical mapping effort.

Physical Map

The distance between sites on physical maps is measured in units of physical length, such as numbers of nucleotide pairs. One type describes the order and spacing of markers on a DNA molecule such as the cytogenetic map(low resolution 10x 106basepairs) the long range restriction map (higher resolution 100,000 2x106basepairs). The second type of physical map consists of a collection of cloned pieces of DNA that represent a complete chromosome or chromosomal segment, together with information about the order of the cloned pieces. A collection of ordered clones is typically the starting material for sequencing. there are still several technological barriers to the rapid, inexpensive, and routine construction of physical maps. Typically contigs are small, the length of DNA over which the physical map shows continuity , or "connectivity," must be considerably longer. Another difficulty faced by those trying to assemble physical maps of chromosomes has been the inability to compare the results of one mapping method directly with those of another and to combine maps constructed by two different techniques into a single map. This problem is addressed by reporting data from any of a variety of physical mapping techniques in a common "language". Each mapped element (individual clone, contig, or sequenced region) is defined by a unique "sequence-tagged site" or STS, which is basically a short DNA sequence that has been shown to be unique. A map is then constructed showing the order and spacing of the STS's. This will also facilitate the integration of results from different laboratories, regardless of the methods used, to produce a single, useful physical map and will establish a uniform criterion for determining how complete the map of a particular region is. Finally, an STS map may in the future be the appropriate starting point for sequencing of DNA. In addition the STS map can be represented electronically and stored in a database that is publicly available and contains sufficient information to enable any scientist to recover de novo any mapped chromosomal region in his/her own laboratory.
 

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