A METHOD FOR GENOME COMPARISONS AND HYBRIDIZATION STUDIES USING KNOWNMEGABASE-SCALE DNA-SEQUENCES AS A REFERENCE

We present a method for genome comparisons and high-resolution hybridi zation analyses using megabase stretches of known DNA sequences as a r eference, The method employs two-dimensional gel electrophoresis, sepa rating genomic segments cut with different restriction endonucleases i n the first and second dimensions, to generate filters suitable for im age analysis and repeated nucleic acid hybridizations. The correspondi ng two-dimensional pattern is computed from the reference nucleotide s equence and matched to the observed pattern, thereby identifying each fragment on the filter; at the same time the technique uncovers discre pancies from the reference sequence, This permits genome comparisons a s well as automated identification and quantification of hybridization patterns with various probes, The technique is illustrated by an anal ysis of Saccharomyces cerevisiae chromosome IX. (C) 1997 Academic Pres s.