title: An oligo-screening strategy to fill gaps found during shotgun sequencing projects.
abstract: During the course of projects to sequence human and nematode cosmids we encountered 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 flanking the gap, clones are identified that contiguate the cosmid sequence. Our method has been integrated into the GAP4 sequence assembly program. The strategy reduces both time and costs in large scale sequencing projects.
authors.affiliation: Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, England.
authors.forename: J
authors.initials: J
authors.lastname: Flint
authors.forename: M
authors.initials: M
authors.lastname: Sims
authors.forename: K
authors.initials: K
authors.lastname: Clark
authors.forename: R
authors.initials: R
authors.lastname: Staden
authors.forename: K
authors.initials: K
authors.lastname: Thomas
mesh_terms: D000818:Animals; D003360:Cosmids / Q000235:genetics; D015723:Gene Library; D016678:Genome; D006801:Humans; D009348:Nematoda / Q000235:genetics; D009838:Oligodeoxyribonucleotides / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D009838:Oligodeoxyribonucleotides