Dna Sequence Assembly Involving an Acyclic Graph Model

Jacek Blazewicz, Wojciech Frohmberg, Piotr Gawron, Marta Kasprzak, Michal Kierzynka, Aleksandra Swiercz, Pawel Wojciechowski
2013 Foundations of Computing and Decision Sciences  
The problem of DNA sequence assembly is well known for its high complexity. Experimental errors of di erent 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
more » ... al, 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.
doi:10.2478/v10209-011-0019-4 fatcat:rjgi62s2tjav5emnddnhhlx3vu