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Toward Simplifying and Accurately Formulating Fragment Assembly
 JOURNAL OF COMPUTATIONAL BIOLOGY
, 1995
"... The fragment assembly problem is that of reconstructing a DNA sequence from a collection of randomly sampled fragments. Traditionally the objective of this problem has been to produce the shortest string that contains all the fragments as substrings, but in the case of repetitive target sequence ..."
Abstract

Cited by 38 (1 self)
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The fragment assembly problem is that of reconstructing a DNA sequence from a collection of randomly sampled fragments. Traditionally the objective of this problem has been to produce the shortest string that contains all the fragments as substrings, but in the case of repetitive target sequences this objective produces answers that are overcompressed. In this paper, the problem is reformulated as one of finding a maximumlikelihood reconstruction with respect to the 2sided KolmogorovSmirnov statistic, and it is argued that this is a better formulation of the problem. Next the fragment assembly problem is recast in graphtheoretic terms as one of finding a noncyclic subgraph with certain properties and the objectives of being shortest or maximallylikely are also recast in this framework. Finally, a series of graph reduction transformations are given that dramatically reduce the size of the graph to be explored in practical instances of the problem. This reduction is ...