For the positional cloning of genes and other novel types of genetic experiments, in humans and other organisms, there is a crucial need for techniques with which genome-wide high-resolution ordered clone maps can be rapidly constructed. Current best methods, such as sequence-tagged site (STS) content mapping, entail a large number of experiments and, in practice, require large low-resolution yeast artificial chromosome (YAC) clones and very many STSs. In this paper, we introduce a new approach, inner product mapping (IPM), that overcomes these limitations. IPM uses radiation hybrids (RHs) to provide localizing signatures for YACs. Two independent data tables that compare YACs against RHs and RHs against STSs are obtained; these tables are combined to produce a computed map of the YACs against ordered STSs. IPM maps each YAC independently, requires relatively few RH comparisons to map a YAC, and can work with small (or large) YACs and few (or many) STSs. This paper describes IPM and presents computer simulations supporting the efficiency of IPM over that of competing methods.
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