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arXiv 2201.12454cs.DS
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De Bruijn图上近似模式匹配的复杂性

The Complexity of Approximate Pattern Matching on De Bruijn Graphs

Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru

摘要:

将序列与标记图中的行走对齐是计算生物学中一个非常重要的问题。为了在具有$|E|$边的任意图中找到与长度$m$的模式精确匹配的行走,基于强指数时间假设(SETH)的下限意味着明显快于$O(|E|m)$时间的算法是不可能的[Equi等人,ICALP 2019]。然而,对于许多特殊的图,例如de Bruijn图,该问题可以在线性时间内解决[Bowe等人,WABI 2012年]。对于近似匹配,图片更复杂。当只允许对模式进行编辑(替换、插入和删除)时,或者当图是非循环的时,问题也可以在$O(|E|m)$时间内解决。当允许对任意循环图进行编辑时,即使在二进制字母表上,问题也变成NP完全[Jain等人,RECOMB 2019]。即使编辑仅限于替换,这些结果也保持不变。de Bruijn图上的近似模式匹配的复杂性仍然是开放的。我们调查这个问题,并表明,使德Bruijn图服从高效的精确模式匹配的属性不扩展到近似匹配,即使仅限于替换的情况下,字母表大小为4。我们证明了,当允许对de Bruijn图进行替换时,判定图中匹配行走的存在性是NP-完全的。此外,我们证明了一个算法显着快于$O(|E|m)$是不可能的de Bruijn图的情况下,只允许替换的模式。这与模式到文本匹配相反,在模式到文本匹配中,精确匹配在线性时间内可解,如de Bruijn图,但替换下的近似匹配在次二次$O(n\sqrt{m})$时间内可解,其中$n$是文本的长度[Abrahamson,SIAM J. Computing 1987]。

英文摘要:

Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on the Strong Exponential Time Hypothesis (SETH) implies an algorithm significantly faster than $O(|E|m)$ time is unlikely [Equi et al., ICALP 2019]. However, for many special graphs, such as de Bruijn graphs, the problem can be solved in linear time [Bowe et al., WABI 2012]. For approximate matching, the picture is more complex. When edits (substitutions, insertions, and deletions) are only allowed to the pattern, or when the graph is acyclic, the problem is again solvable in $O(|E|m)$ time. When edits are allowed to arbitrary cyclic graphs, the problem becomes NP-complete, even on binary alphabets [Jain et al., RECOMB 2019]. These results hold even when edits are restricted to only substitutions. The complexity of approximate pattern matching on de Bruijn graphs remained open. We investigate this problem and show that the properties that make de Bruijn graphs amenable to efficient exact pattern matching do not extend to approximate matching, even when restricted to the substitutions only case with alphabet size four. We prove that determining the existence of a matching walk in a de Bruijn graph is NP-complete when substitutions are allowed to the graph. In addition, we demonstrate that an algorithm significantly faster than $O(|E|m)$ is unlikely for de Bruijn graphs in the case where only substitutions are allowed to the pattern. This stands in contrast to pattern-to-text matching where exact matching is solvable in linear time, like on de Bruijn graphs, but approximate matching under substitutions is solvable in subquadratic $O(n\sqrt{m})$ time, where $n$ is the text's length [Abrahamson, SIAM J. Computing 1987].

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