A strategy of ''sequence scanning'' is proposed for rapid acquisition of sequence from clones such as bacteriophage P1 clones, cosmids, or yeast artificial chromosomes, The approach makes use of a special vector, called LambdaScan, that reliably yields subclones with inserts in the size range 8-12 kb, A number of subclones, typically 96 or 192, are chosen at random, and the ends of the inserts are sequenced using vector-specific primers, Then long-range spectrum PCR is used to order and orient the clones, This combination of shotgun and directed sequencing results in a high-resolution physical map suitable for the identification of coding regions or for comparison of sequence organization among genomes, Computer simulations indicate that, for a target clone of 100 kb, the scanning of 192 subclones with sequencing reads as short as 350 bp results in an approximate ratio of 1:2:1 of regions of double-stranded sequence, single-stranded sequence, and gaps, Longer sequencing reads tip the ratio strongly toward increased double-stranded sequence.
