Greedy shortest common superstring approximation in compact space

DOI10.1007/978-3-319-67428-5_1MaRDI QIDQ5150914zbMATH OpenOpenAlexFDO

Authors Jarno Alanko, Tuukka Norri

Publication date 16 February 2021

Published in String Processing and Information Retrieval (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1707.07727

zbMATH Keywords

Burrows-Wheeler transformBWTcompact spacegreedy approximationSCSshortest common superstringspace-efficient

Mathematics Subject Classification ID

Algorithms on strings (68W32)

Abstract: Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for solving the problem. We present the first time and space efficient implementation of the classic greedy heuristic which merges strings in decreasing order of overlap length. Our implementation works in $O(nlogsigma)$ time and bits of space, where $n$ is the total length of the input strings in characters, and $sigma$ is the size of the alphabet. After index construction, a practical implementation of our algorithm uses roughly $5nlogsigma$ bits of space and reasonable time for a real dataset that consists of DNA fragments.

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Cites work

• A greedy approximation algorithm for constructing shortest common superstrings
• A linear-time algorithm for a special case of disjoint set union
• A linear-time algorithm for finding approximate shortest common superstrings
• Approximation algorithms for the shortest common superstring problem
• Introduction to algorithms
• Linear time construction of compressed text indices in compact space
• Lyndon words and short superstrings
• On finding minimal length superstrings
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Cited in

(3)

• Why greed works for shortest common superstring problem
• scientific article; zbMATH DE number 1263192 (Why is no real title available?)
• Compressed Multiple Pattern Matching

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