Levels of clone and sequence coverage.

A fingerprint clone contig is assembled by using the computer program FPC84,451 to analyze the restriction enzyme digestion patterns of many large-insert clones. Clones are then selected for sequencing to minimize overlap between adjacent clones. For a clone to be selected, all of its restriction enzyme fragments (except the two vector-insert junction fragments) must be shared with at least one of its neighbors on each side in the contig. Once these overlapping clones have been sequenced, the set is a sequenced-clone contig. When all selected clones from a fingerprint clone contig have been sequenced, the sequenced-clone contig will be the same as the fingerprint clone contig. Until then, a fingerprint clone contig may contain several sequenced-clone contigs. After individual clones (for example, A and B) have been sequenced to draft coverage and the clones have been mapped, the data are analyzed by GigAssembler, producing merged sequence contigs from initial sequence contigs, and linking these to form sequence-contig scaffolds.