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Algorithms 2015, 8(3), 754-773; doi:10.3390/a8030754

Modified Classical Graph Algorithms for the DNA Fragment Assembly Problem

1
Engineering Department, Universidad Iberoamericana Ciudad de México, Prolongación Paseo de la Reforma 880, Lomas de Santa Fe, Distrito Federal 01219, Mexico
2
Universidad Iberoamericana Ciudad de México, DCI, Prolongación Paseo de la Reforma 880, Lomas de Santa Fe, Distrito Federal 01219, Mexico
3
Physics and Mathematics Department, Universidad Iberoamericana Ciudad de México, Prolongación Paseo de la Reforma 880, Lomas de Santa Fe, Distrito Federal 01219, Mexico
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editors: Giuseppe Lancia and Alberto Policriti
Received: 24 June 2015 / Revised: 6 August 2015 / Accepted: 26 August 2015 / Published: 10 September 2015
(This article belongs to the Special Issue Algorithmic Themes in Bioinformatics)
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Abstract

DNA fragment assembly represents an important challenge to the development of efficient and practical algorithms due to the large number of elements to be assembled. In this study, we present some graph theoretical linear time algorithms to solve the problem. To achieve linear time complexity, a heap with constant time operations was developed, for the special case where the edge weights are integers and do not depend on the problem size. The experiments presented show that modified classical graph theoretical algorithms can solve the DNA fragment assembly problem efficiently. View Full-Text
Keywords: DNA fragment assembly; minimum spanning tree; heap; linear complexity DNA fragment assembly; minimum spanning tree; heap; linear complexity
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Mallén-Fullerton, G.M.; Quiroz-Ibarra, J.E.; Miranda, A.; Fernández-Anaya, G. Modified Classical Graph Algorithms for the DNA Fragment Assembly Problem. Algorithms 2015, 8, 754-773.

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