Optimal computation of avoided words

DOI10.1007/978-3-319-43681-4_1MaRDI QIDQ1708407zbMATH OpenOpenAlexFDO

Authors Yannis Almirantis, Panagiotis Charalampopoulos, Jia Gao, Costas S. Iliopoulos, Manal Mohamed, Solon P. Pissis, Dimitris Polychronopoulos

Publication date 23 March 2018

Full work available at URL https://arxiv.org/abs/1604.08760

zbMATH Keywords

\(\rho \)-avoided wordsDNA linguistic analysis

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Algebraic theory of languages and automata (68Q70) Computational methods for problems pertaining to biology (92-08)

Abstract: The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of the standard deviation of $w$, denoted by $std(w)$, effectively characterises the extent of a word by its edge contrast in the context in which it occurs. A word $w$ of length $k>2$ is a $ho$-avoided word in $x$ if $std(w)leqho$, for a given threshold $ho<0$. Notice that such a word may be completely absent from $x$. Hence computing all such words na"{i}vely can be a very time-consuming procedure, in particular for large $k$. In this article, we propose an $O(n)$-time and $O(n)$-space algorithm to compute all $ho$-avoided words of length $k$ in a given sequence $x$ of length $n$ over a fixed-sized alphabet. We also present a time-optimal $O(sigman)$-time and $O(sigman)$-space algorithm to compute all $ho$-avoided words (of any length) in a sequence of length $n$ over an alphabet of size $sigma$. Furthermore, we provide a tight asymptotic upper bound for the number of $ho$-avoided words and the expected length of the longest one. We make available an open-source implementation of our algorithm. Experimental results, using both real and synthetic data, show the efficiency of our implementation.

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(2)

• On overabundant words and their application to biological sequence analysis
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