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In the process of constructing high-resolution restriction maps via greedy algorithms, a classical anomaly, known as fragment collapsing, introduces errors into the maps that impedes further map assembly. Fragment collapsing occurs when two different genomic fragments of approximately the same length and occurring in the digestion of two different overlapping clones are incorrectly identified as representative of a single genomic fragment. This introduces a single fragment of commensurate length into an incorrect position in the map. The present work describes techniques for detecting and correcting such anomalies.

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We examine a problem that arises in physical DNA mapping, namely determining what common DNA is represented in two maps. We present an example illustrating the properties of DNA mapping, and motivate our approach. We present a new graph structure, called the Ƶ-graph, that takes advantage of structure that develops during the mapping process, thus catalyzing the discovery of all relevant fragment matchings. We describe an algorithm based on this structure and present experimental data supporting its improved performance as compared with a naive approach.

No abstract