EXPECTATION AND VARIANCE OF TRUE AND FALSE FRAGMENT MATCHES IN DNA RESTRICTION MAPPING

Consider a DNA mapping project in which overlap of clones is inferred from multiple complete restriction enzyme digests. Each enzyme cuts ea ch clone randomly into fragments whose lengths are determined with som e error, Clones that share fragments with matching lengths could conta in a region of overlap, However, common fragment lengths may be due to random coincidence leading to a false overlap declaration. Although t he probability of false fragment matching is small, a mapping project involves a large number of clone comparisons, Consequently, erroneous fragment matches can be a serious problem. We use a geometrical probab ility approach to develop exact integral formulas and first-order appr oximations for the expected number and variance of classes of fragment pairs that will be identified falsely as matching, We also find exact formulas for the expected value, and variance of the number of true f ragment matches, These formulas are useful in comparing different mapp ing strategies.