MAPPING GENES WITHIN A YAC BY COMPUTER-ASSISTED INTERPRETATION OF PARTIAL RESTRICTION DIGESTIONS

Partial restriction digestion is used to map restriction sites and the location of genes within yeast artificial chromosomes (YACs), Locus-s pecific probes are hybridised to the partially digested YAC DNA and th e fragments to which they hybridise are compared with the pattern of p artial digestion products that include each map region, A least square s criterion is presented which allows for error in fragment length det ermination, This rapidly defines the most likely location of a marker within the restriction map and permits the combination of results from digestions with different restriction enzymes, Approximate confidence intervals may be assigned to gene locations, and tests of goodness-of -fit of the data may be performed, Since the number of erroneously mat ched fragments increases in proportion to the square of the number of sites, denser maps are not necessarily more informative, Simulations i ndicate that the optimal number of internal restriction sites given ty pical experimental error (1% of YAC length) is about five sites; the a ssociated broad support interval (on average one third of YAC length) may be reduced by combining results from different enzyme digestions. Application of a computer implementation of this model to experimental data showed that the model fitted well, and estimates of location wer e found to be consistent with other evidence.