DNA Sequence Homology Estimation by Combinatorial Analysis of Endonuclease Restriction Data

Abstract

A combinatorial analysis of the products of DNA cleavage by restriction endonucleases permits an estimation of the sequence homology between closely related linear DNAs. The main assumption to be made is that fragments of identical length represent equivalent sections of the genomes. All patterns of common and varying restriction sites compatible with the results of the electrophoretic analysis of fragment sizes can be enumerated, each yielding an estimate of the proportion of sequences of restriction site length common to both DNAs. From this, sequence homology is derived by using a model of randomly distributed point mutations relating the two genomes. Possible limitations of the approach are discussed.