An oligo-screening strategy to fill gaps found during shotgun sequencing projects

During the course of projects to sequence human and nematode cosmids we enc ountered great difficulties generating contiguous sequence in regions with repetitive DNA (Alu repeats in humans and tandem or inverted repeats in the nematode). We have developed a simple and efficient strategy to fill gaps. By screening M13, plasmid or phagemid libraries with oligonucleotides flan king the gap, clones are identified that contiguate the cosmid sequence. Ou r method has been integrated into the GAP4 sequence assembly program. The s trategy reduces both time and costs in large scale sequencing projects.