Fragment collapsing and splitting while assembling high-resolution restriction maps.

Abstract

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.