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About this paper
Maria Constantin, Adrian Miclăuş, Alexandru Popa
Non-uniform translocation distance is shown to be computationally difficult for string-based genome models that allow repeated symbols: both contiguous and non-contiguous variants are NP-hard, even with a single target string. For the contiguous single-target case, a target-length-dependent kernel and bounded-depth search yield an exact fixed-parameter algorithm with running time e^{O(q^3)}poly(|I|).
Key insights
- The optimization difficulty persists with only one target string, so it arises from duplicated symbols and non-uniform cut choices rather than from a large target set alone.
- Allowing produced strings to be reused does not eliminate the structural constraints captured by the hardness reduction.
- Only substrings compatible with the target need to be retained for the contiguous single-target problem; irrelevant material can be replaced by separators without changing the optimum.
Summary by alphaXiv.
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