Chromosome-specific DNA libraries have been of considerable utility in mapping the human genome. However, conventionally sorted libraries are expensive to produce and are frequently contaminated with other sequences. We propose to use a new methodology, denoted coincidence cloning, to produce chromosome specific libraries from a somatic cell hybrid that contains part of the short arm of human chromosome 4 and most of human chromosome 5. We shall assess the efficiency of four modifications of this technology in constructing such a library and shall characterize the sequence content and representation of these libraries. Mouse chromosomes to date have been refractory to currently available sorting techniques. We shall therefore construct a chromosome specific library from a somatic cell hybrid that contains the tip of mouse chromosome 16 and the majority of mouse chromosome 2. Linking libraries that contain rare cutting restriction enzyme sites will also be constructed from both the human and mouse chromosomes 2. Linking clones will then be used to construct a physical map of overlapping fragments and to derive a genetic map of these markers on the two chromosomes.