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- W4302179634 abstract "We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending positions of substrings in $T$ that match $P$. This problem is a basic primitive in computational biology applications. Let $m$ and $n$ be the lengths of $P$ and $T$, respectively, and let $k$ be the number of strings in $P$. We present a new algorithm achieving time $O(nlog k + m +alpha)$ and space $O(m + A)$, where $A$ is the sum of the lower bounds of the lengths of the gaps in $P$ and $alpha$ is the total number of occurrences of the strings in $P$ within $T$. Compared to the previous results this bound essentially achieves the best known time and space complexities simultaneously. Consequently, our algorithm obtains the best known bounds for almost all combinations of $m$, $n$, $k$, $A$, and $alpha$. Our algorithm is surprisingly simple and straightforward to implement. We also present algorithms for finding and encoding the positions of all strings in $P$ for every match of the pattern." @default.
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- W4302179634 date "2011-10-13" @default.
- W4302179634 modified "2023-09-27" @default.
- W4302179634 title "String Matching with Variable Length Gaps" @default.
- W4302179634 doi "https://doi.org/10.48550/arxiv.1110.2893" @default.
- W4302179634 hasPublicationYear "2011" @default.
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