论文标题

在非标准匹配模型中计算最大的pelindromes

Computing maximal palindromes in non-standard matching models

论文作者

Mieno, Takuya, Funakoshi, Mitsuru, Nakashima, Yuto, Inenaga, Shunsuke, Bannai, Hideo, Takeda, Masayuki

论文摘要

文本数据处理,生物信息学和单词组合学是流行的和重要的对象。令$ s = xay $是一个字符串,其中$ x $和$ y $的长度相同,而$ a $是单个字符或空字符串。然后,存在两个针对alindromes的替代定义:如果$ s $等于其反转$ s^r $(基于反转的定义),则说$ s $是回文。或者,如果其右臂$ y $等于其左臂$ x^r $的反转(基于对称的定义)。显然,如果两个定义中使用的``equality''($ \ of约$)是确切的字符匹配($ = $),则两个定义是相同的。但是,如果我们应用其他弦乐平等标准$ \约$,包括生物学序列的补充匹配模型,笛卡尔树模型[Park等,TCS 2020],参数化模型[Baker,JCSS 1996]基于逆转的回文和基于对称性的alindromes是否相同?据我们所知,以前的工作都没有考虑或回答这个自然问题。在本文中,我们首先提供了这个问题的答案,然后提出有效的算法,用于计算给定字符串中非标准匹配模型下的所有最大alnindromes。 After confirming that Gusfield's offline suffix-tree-based algorithm for computing maximal symmetry-based palindromes can be readily extended to the aforementioned matching models, we show how to extend Manacher's online algorithm for computing maximal reversal-based palindromes in linear time for all the aforementioned matching models.

Palindromes are popular and important objects in textual data processing, bioinformatics, and combinatorics on words. Let $S = XaY$ be a string where $X$ and $Y$ are of the same length, and $a$ is either a single character or the empty string. Then, there exist two alternative definitions for palindromes: $S$ is said to be a palindrome if $S$ is equal to its reversal $S^R$ (Reversal-based definition); or if its right-arm $Y$ is equal to the reversal of its left-arm $X^R$ (Symmetry-based definition). It is clear that if the ``equality'' ($\approx$) used in both definitions is exact character matching ($=$), then the two definitions are the same. However, if we apply other string-equality criteria $\approx$, including the complementary-matching model for biological sequences, the Cartesian-tree model [Park et al., TCS 2020], the parameterized model [Baker, JCSS 1996], the order-preserving model [Kim et al., TCS 2014], and the palindromic-structure model [I et al., TCS 2013], then are the reversal-based palindromes and the symmetry-based palindromes the same? To the best of our knowledge, no previous work has considered or answered this natural question. In this paper, we first provide answers to this question, and then present efficient algorithms for computing all maximal palindromes under the non-standard matching models in a given string. After confirming that Gusfield's offline suffix-tree-based algorithm for computing maximal symmetry-based palindromes can be readily extended to the aforementioned matching models, we show how to extend Manacher's online algorithm for computing maximal reversal-based palindromes in linear time for all the aforementioned matching models.

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