Abstract
The double-cut-and-join operation (DCJ) is a fundamental graph operation that is used to model a variety of genome rearrangements. However, DCJs are only useful when comparing genomes with equal (or nearly equal) gene content. One obvious extension of the DCJ framework supplements DCJs with insertions and deletions of chromosomes and chromosomal intervals, which implies a model in which DCJs receive unit cost, whereas insertions and deletions receive a nonnegative cost of ω. This paper proposes a unified model finding a minimum-cost transformation of one genome (with circular chromosomes) into another genome for any value of ω. In the process, it resolves the open case ω > 1.
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Compeau, P.E.C. (2014). A Generalized Cost Model for DCJ-Indel Sorting. In: Brown, D., Morgenstern, B. (eds) Algorithms in Bioinformatics. WABI 2014. Lecture Notes in Computer Science(), vol 8701. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-44753-6_4
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DOI: https://doi.org/10.1007/978-3-662-44753-6_4
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