MersV1, Main, Exploration, bibRecord, 001D49

An Elegant Algorithm for the Construction of Suffix Arrays.

Identifieur interne : 001D49 ( Main/Exploration ); précédent : 001D48; suivant : 001D50

An Elegant Algorithm for the Construction of Suffix Arrays.

Auteurs : Sanguthevar Rajasekaran [États-Unis] ; Marius Nicolae [États-Unis]

Source :

Journal of discrete algorithms (Amsterdam, Netherlands) [ 1570-8667 ] ; 2014.

RBID : pubmed:25045344

Abstract

The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array consists of the sorted suffixes of a string. There are several linear time suffix array construction algorithms (SACAs) known in the literature. However, one of the fastest algorithms in practice has a worst case run time of O(n²). The problem of designing practically and theoretically efficient techniques remains open. In this paper we present an elegant algorithm for suffix array construction which takes linear time with high probability; the probability is on the space of all possible inputs. Our algorithm is one of the simplest of the known SACAs and it opens up a new dimension of suffix array construction that has not been explored until now. Our algorithm is easily parallelizable. We offer parallel implementations on various parallel models of computing. We prove a lemma on the ℓ-mers of a random string which might find independent applications. We also present another algorithm that utilizes the above algorithm. This algorithm is called RadixSA and has a worst case run time of O(n log n). RadixSA introduces an idea that may find independent applications as a speedup technique for other SACAs. An empirical comparison of RadixSA with other algorithms on various datasets reveals that our algorithm is one of the fastest algorithms to date. The C++ source code is freely available at http://www.engr.uconn.edu/~man09004/radixSA.zip.

DOI: 10.1016/j.jda.2014.03.001
PubMed: 25045344

Affiliations:

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<front><div type="abstract" xml:lang="en">The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array consists of the sorted suffixes of a string. There are several linear time suffix array construction algorithms (SACAs) known in the literature. However, one of the fastest algorithms in practice has a worst case run time of <i>O</i>
(<i>n</i>
<sup>2</sup>
). The problem of designing practically and theoretically efficient techniques remains open. In this paper we present an elegant algorithm for suffix array construction which takes linear time with high probability; the probability is on the space of all possible inputs. Our algorithm is one of the simplest of the known SACAs and it opens up a new dimension of suffix array construction that has not been explored until now. Our algorithm is easily parallelizable. We offer parallel implementations on various parallel models of computing. We prove a lemma on the ℓ-mers of a random string which might find independent applications. We also present another algorithm that utilizes the above algorithm. This algorithm is called RadixSA and has a worst case run time of <i>O</i>
(<i>n</i>
 log <i>n</i>
). RadixSA introduces an idea that may find independent applications as a speedup technique for other SACAs. An empirical comparison of RadixSA with other algorithms on various datasets reveals that our algorithm is one of the fastest algorithms to date. The C++ source code is freely available at http://www.engr.uconn.edu/~man09004/radixSA.zip.</div>
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An Elegant Algorithm for the Construction of Suffix Arrays.

An Elegant Algorithm for the Construction of Suffix Arrays.

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