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DNA sequence assembly involving an acyclic graph model

Blazewicz J., Frohmberg W., Gawron P., Kasprzak M., Kierzynka M., Swiercz A, Wojciechowski P.

Foundations of Computing and Decision Sciences

2013

Vol. 38, No. 1

25--34

The problem of DNA sequence assembly is well known for its high complexity. Experimental errors of different kinds present in data and huge sizes of the problem instances make this problem very hard to solve. In order to deal with such data, advanced efficient heuristics must be constructed. Here, we propose a new approach to the sequence assembly problem, modeled as the problem of searching for paths in an acyclic digraph. Since the graph representing an assembly instance is not acyclic in general, it is heuristically transformed into the acyclic form. This approach reduces the time of computations significantly and allows to maintain high quality of produced solutions.