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arXiv · 2305.01851

Complexity and Enumeration in Models of Genome Rearrangement

Lora Bailey·Heather Smith Blake·Garner Cochran·Nathan Fox·Michael Levet·Reem Mahmoud·Elizabeth Matson·Inne Singgih·Grace Stadnyk·Xinyi Wang·Alexander Wiedemann
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Abstract

In this paper, we examine the computational complexity of enumeration in certain genome rearrangement models. We first show that the Pairwise Rearrangement problem in the Single Cut-and-Join model (Bergeron, Medvedev, & Stoye, J. Comput. Biol. 2010) is $\#\textsf{P}$-complete under polynomial-time Turing reductions. Next, we show that in the Single Cut or Join model (Feijao & Meidanis, IEEE ACM Trans. Comp. Biol. Bioinf. 2011), the problem of enumerating all medians ($\#$Median) is logspace-computable ($\textsf{FL}$), improving upon the previous polynomial-time ($\textsf{FP}$) bound of Mikl\'os & Smith (RECOMB 2015).

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Lora Bailey, Heather Smith Blake, Garner Cochran, Nathan Fox, Michael Levet, Reem Mahmoud, Elizabeth Matson, Inne Singgih, Grace Stadnyk, Xinyi Wang, Alexander Wiedemann. 2023-05-03. Complexity and Enumeration in Models of Genome Rearrangement. https://doi.org/10.1016/j.tcs.2024.114880

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