The CHEF-DR III system separates large and small DNA fragments with better resolution, speed, and accuracy, than initial pulsed field methods. DNAs from 100 bases to over 10 megabases (mb) may be effectively resolved. For example, the chromosomal DNA of Schizosaccharomyces pombe can be resolved in 1 day using a 106° pulse angle, compared to 2 days at 120°. Everything from Yeast Artificial Chromosomes (YACs) to M13 inserts can be separated with a single instrument. Applications include top down and bottom up mapping electrophoretic karyotyping, analysis of tumor cell DNA rearrangements, mammalian DNA analysis, and testing for bacterial, yeast, and parasite strain homogeneity.