Summary: Restriction Site Mapping is in Separation Theory.
L. Allison and C. N. Yee
Department of Computer Science, Monash University, Clayton, Victoria, Australia 3168.
Written: 29July 1987; Revised: 27October; Printed: September 22, 2004
Appeared in Nucleic Acids Research/ Computer Applications in the Biosciences (CABIOS) special issue
CABIOS 4(1) 97101 Jan 1988
A computer algorithm for restrictionsite mapping consists of a generator of partial maps and a
consistency checker. This paper examines consistency checking and argues that a method based on
separation theory extracts the maximum amount of information from fragment lengths in digest data. It
results in the minimum number of false maps being generated.
Restrictionsite mapping involves locating certain restriction sites on a circular plasmid, on a linear
phage or on some other sequence of DNA. The raw data for the problem consist of fragment lengths from
one or more digests carried out on the DNA. Deducing the map is a combinatorial problem often
performed with the aid of a computer program [1-9]. While there is only one real map, the data can
suggest several, perhaps a great many, maps particularly when experimental errors are considered. It is
very important that no map consistent with the data is missed. It is almost equally important that every
effort be taken to suppress inconsistent maps which could swamp the experimenter.
This paper examines the problem of placing the strongest constraints, that can be deduced from the