Application of a MAX-CUT Heuristic to the Contig Orientation Problem in Genome Assembly

Authors:
Paul Bodily;Mark J. Clement;Quinn Snell;Jared C. Price;Stanley Fujimoto;Nozomu Okuda
Affiliations:
CS Department, Brigham Young University, 3361 TMCB PO Box 26576, Provo, UT 84602-6576;CS Department, Brigham Young University, 3361 TMCB PO Box 26576, Provo, UT 84602-6576;CS Department, Brigham Young University, 3361 TMCB PO Box 26576, Provo, UT 84602-6576;CS Department, Brigham Young University, 3361 TMCB PO Box 26576, Provo, UT 84602-6576;CS Department, Brigham Young University, 3361 TMCB PO Box 26576, Provo, UT 84602-6576;CS Department, Brigham Young University, 3361 TMCB PO Box 26576, Provo, UT 84602-6576
Venue:
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Year:
2013

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Abstract

In the context of genome assembly, the contig orientation problem is described as the problem of removing sufficient edges from the scaffold graph so that the remaining subgraph assigns a consistent orientation to all sequence nodes in the graph. This problem can also be phrased as a weighted MAX-CUT problem. The performance of MAX-CUT heuristics in this application is untested. We present a greedy heuristic solution to the contig orientation problem and compare its performance to a weighted MAX-CUT semi-definite programming heuristic solution on several graphs. We note that the contig orientation problem can be used to identify inverted repeats and inverted haplotypes, as these represent sequences whose orientation appears ambiguous in the conventional genome assembly framework.