Engineering a Lightweight External Memory Suffix Array Construction Algorithm
We describe an external memory suffix array construction algorithm based on constructing suffix arrays for blocks of text and merging them into the full suffix array. The basic idea goes back over 20 years and there has been a couple of later improvements, but we describe several further improvement...
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| Published in | Mathematics in computer science Vol. 11; no. 2; pp. 137 - 149 |
|---|---|
| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
Cham
Springer International Publishing
01.06.2017
Springer Nature B.V |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1661-8270 1661-8289 |
| DOI | 10.1007/s11786-016-0281-1 |
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| Abstract | We describe an external memory suffix array construction algorithm based on constructing suffix arrays for blocks of text and merging them into the full suffix array. The basic idea goes back over 20 years and there has been a couple of later improvements, but we describe several further improvements that make the algorithm much faster. In particular, we reduce the I/O volume of the algorithm by a factor
O
log
σ
n
. Our experiments show that the algorithm is the fastest suffix array construction algorithm when the size of the text is within a factor of about five from the size of the RAM in either direction, which is a common situation in practice. |
|---|---|
| AbstractList | We describe an external memory suffix array construction algorithm based on constructing suffix arrays for blocks of text and merging them into the full suffix array. The basic idea goes back over 20 years and there has been a couple of later improvements, but we describe several further improvements that make the algorithm much faster. In particular, we reduce the I/O volume of the algorithm by a factor O log σ n . Our experiments show that the algorithm is the fastest suffix array construction algorithm when the size of the text is within a factor of about five from the size of the RAM in either direction, which is a common situation in practice. We describe an external memory suffix array construction algorithm based on constructing suffix arrays for blocks of text and merging them into the full suffix array. The basic idea goes back over 20 years and there has been a couple of later improvements, but we describe several further improvements that make the algorithm much faster. In particular, we reduce the I/O volume of the algorithm by a factor O log σ n . Our experiments show that the algorithm is the fastest suffix array construction algorithm when the size of the text is within a factor of about five from the size of the RAM in either direction, which is a common situation in practice. |
| Author | Kärkkäinen, Juha Kempa, Dominik |
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| Keywords | 68W32 (Algorithms on strings) External memory algorithms Algorithm engineering Suffix array construction |
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| References | Kärkkäinen (CR14) 2007; 387 CR19 CR18 CR17 CR16 CR15 Kärkkäinen, Sanders, Burkhardt (CR20) 2006; 53 Abouelhoda, Kurtz, Ohlebusch (CR1) 2004; 2 CR10 Gonnet, Baeza-Yates, Snider, Frakes, Baeza-Yates (CR13) 1992 Williams, Zobel (CR31) 1999; 42 Ferragina, Manzini (CR12) 2005; 52 Crauser, Ferragina (CR7) 2002; 32 Vitter (CR30) 2006; 2 Knuth, Morris, Pratt (CR21) 1977; 6 CR2 CR4 CR3 CR6 CR5 Crochemore (CR8) 1992; 92 CR29 CR28 CR9 CR27 CR25 CR24 CR23 Ohlebusch (CR26) 2013 Ferragina, Gagie, Manzini (CR11) 2012; 63 Manber, Myers (CR22) 1993; 22 M Crochemore (281_CR8) 1992; 92 P Ferragina (281_CR11) 2012; 63 281_CR29 281_CR28 281_CR27 A Crauser (281_CR7) 2002; 32 281_CR25 E Ohlebusch (281_CR26) 2013 281_CR24 281_CR23 DE Knuth (281_CR21) 1977; 6 GH Gonnet (281_CR13) 1992 J Kärkkäinen (281_CR20) 2006; 53 HE Williams (281_CR31) 1999; 42 MI Abouelhoda (281_CR1) 2004; 2 JS Vitter (281_CR30) 2006; 2 281_CR19 281_CR18 281_CR17 281_CR16 J Kärkkäinen (281_CR14) 2007; 387 281_CR15 281_CR2 P Ferragina (281_CR12) 2005; 52 281_CR10 281_CR9 281_CR4 281_CR3 281_CR6 281_CR5 U Manber (281_CR22) 1993; 22 |
| References_xml | – ident: CR18 – ident: CR4 – ident: CR2 – ident: CR16 – volume: 53 start-page: 918 issue: 6 year: 2006 end-page: 936 ident: CR20 article-title: Linear work suffix array construction publication-title: J. ACM doi: 10.1145/1217856.1217858 – volume: 6 start-page: 323 issue: 2 year: 1977 end-page: 350 ident: CR21 article-title: Fast pattern matching in strings publication-title: SIAM J. Comput. doi: 10.1137/0206024 – ident: CR10 – volume: 2 start-page: 305 issue: 4 year: 2006 end-page: 474 ident: CR30 article-title: Algorithms and data structures for external memory publication-title: Found. Trends Theor. Comput. Sci. doi: 10.1561/0400000014 – ident: CR6 – ident: CR29 – volume: 2 start-page: 53 issue: 1 year: 2004 end-page: 86 ident: CR1 article-title: Replacing suffix trees with enhanced suffix arrays publication-title: J. 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| SubjectTerms | Algorithms Computer Science Mathematics Mathematics and Statistics Random access memory |
| Title | Engineering a Lightweight External Memory Suffix Array Construction Algorithm |
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