title: A method for genome comparisons and hybridization studies using known megabase-scale DNA sequences as a reference.
abstract: We present a method for genome comparisons and high-resolution hybridization analyses using megabase stretches of known DNA sequences as a reference. The method employs two-dimensional gel electrophoresis, separating genomic segments cut with different restriction endonucleases in the first and second dimensions, to generate filters suitable for image analysis and repeated nucleic acid hybridizations. The corresponding two-dimensional pattern is computed from the reference nucleotide sequence and matched to the observed pattern, thereby identifying each fragment on the filter; at the same time the technique uncovers discrepancies from the reference sequence. This permits genome comparisons as well as automated identification and quantification of hybridization patterns with various probes. The technique is illustrated by an analysis of Saccharomyces cerevisiae chromosome IX.
authors.affiliation: Department of Molecular Biology and Oncology, University of Texas Southwestern Medical Center, Dallas 75235-9140, USA.
authors.forename: P
authors.initials: P
authors.lastname: Qiu
authors.forename: K C
authors.initials: KC
authors.lastname: Kupfer
authors.forename: W T
authors.initials: WT
authors.lastname: Garrard
mesh_terms: D016386:Chromosome Walking / Q000379:methods; D015825:Chromosomes, Fungal; D003196:Computer Graphics; D004247:DNA / Q000032:analysis; D004262:DNA Restriction Enzymes / Q000378:metabolism; D015180:Electrophoresis, Gel, Two-Dimensional; D005374:Filtration / Q000295:instrumentation; D005800:Genes, Fungal; D007091:Image Processing, Computer-Assisted; D017403:In Situ Hybridization / Q000379:methods; D009693:Nucleic Acid Hybridization / Q000379:methods*; D012016:Reference Values; D012107:Research Design; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000592:standards*
chemical_list: D004247:DNA; D004262:DNA Restriction Enzymes