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Volumn 6, Issue 2, 2013, Pages 319-351

Practical compressed suffix trees

Author keywords

Bioinformatics; Compressed data structures; Repetitive sequence collections; Suffix trees

Indexed keywords

COMPRESSED DATA STRUCTURES; COMPRESSED SUFFIX TREES; LARGE SEQUENCES; MIN-MAX; RECENT RESEARCHES; REPETITIVE SEQUENCE COLLECTIONS; SPACE-TIME TRADEOFFS; SUFFIX-TREES;

EID: 84880439157     PISSN: None     EISSN: 19994893     Source Type: Journal    
DOI: 10.3390/a6020319     Document Type: Article
Times cited : (34)

References (51)
  • 1
    • 84880438036 scopus 로고    scopus 로고
    • MIT Technology Review
    • Available online:(accessed on 20 May 2013)
    • MIT Technology Review. Available online: http://www.technologyreview.com/featuredstory/511051/ inside-chinas-genome-factory (accessed on 20 May 2013).
  • 2
    • 0016942292 scopus 로고
    • A space-economical suffix tree construction algorithm
    • McCreight, E. A space-economical suffix tree construction algorithm. J. ACM 1976, 32, 262-272.
    • (1976) J. ACM , vol.32 , pp. 262-272
    • McCreight, E.1
  • 4
    • 0002139526 scopus 로고
    • The Myriad Virtues of Subword Trees
    • In Combinatorial Algorithms on Words; Springer-Verlag: Berlin, Germany
    • Apostolico, A. The Myriad Virtues of Subword Trees. In Combinatorial Algorithms on Words; Springer-Verlag: Berlin, Germany, 1985; pp. 85-96.
    • (1985) , pp. 85-96
    • Apostolico, A.1
  • 5
    • 0004137004 scopus 로고    scopus 로고
    • Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology
    • Cambridge University Press: Cambridge, UK
    • Gusfield, D. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology; Cambridge University Press: Cambridge, UK, 1997.
    • (1997)
    • Gusfield, D.1
  • 6
    • 0033227559 scopus 로고    scopus 로고
    • Reducing the space requirements of suffix trees
    • Kurtz, S. Reducing the space requirements of suffix trees. Softw. Prac. Exp. 1999, 29, 1149-1171.
    • (1999) Softw. Prac. Exp. , vol.29 , pp. 1149-1171
    • Kurtz, S.1
  • 7
    • 0027681165 scopus 로고
    • Suffix arrays: A new method for on-line string searches
    • Manber, U.; Myers, E. Suffix arrays: A new method for on-line string searches. SIAM J. Comput. 1993, 22, 935-948.
    • (1993) SIAM J. Comput. , vol.22 , pp. 935-948
    • Manber, U.1    Myers, E.2
  • 9
    • 0000674707 scopus 로고    scopus 로고
    • Space efficient suffix trees
    • Munro, I.; Raman, V.; Rao, S. Space efficient suffix trees. J. Algorithms 2001, 39, 205-222.
    • (2001) J. Algorithms , vol.39 , pp. 205-222
    • Munro, I.1    Raman, V.2    Rao, S.3
  • 10
    • 84968866645 scopus 로고    scopus 로고
    • Succinct Representations of Lcp Information and Improvements in the Compressed Suffix Arrays
    • San Francisco, CA, USA, 6-8 January 2002
    • Sadakane, K. Succinct Representations of Lcp Information and Improvements in the Compressed Suffix Arrays. In Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), San Francisco, CA, USA, 6-8 January 2002; pp. 225-232.
    • Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) , pp. 225-232
    • Sadakane, K.1
  • 11
    • 34250183733 scopus 로고    scopus 로고
    • Compressed suffix trees with full functionality
    • Sadakane, K. Compressed suffix trees with full functionality. Theory Comput. Syst. 2007, 41, 589-607.
    • (2007) Theory Comput. Syst. , vol.41 , pp. 589-607
    • Sadakane, K.1
  • 12
    • 0041427690 scopus 로고    scopus 로고
    • New text indexing functionalities of the compressed suffix arrays
    • Sadakane, K. New text indexing functionalities of the compressed suffix arrays. J. Algorithms 2003, 48, 294-313.
    • (2003) J. Algorithms , vol.48 , pp. 294-313
    • Sadakane, K.1
  • 14
    • 80053483441 scopus 로고    scopus 로고
    • Fully-compressed suffix trees
    • doi:10.1145/2000807.2000821
    • Russo, L.; Navarro, G.; Oliveira, A. Fully-compressed suffix trees. ACM Trans. Algorithms 2011, 7, doi:10.1145/2000807.2000821.
    • (2011) ACM Trans. Algorithms , vol.7
    • Russo, L.1    Navarro, G.2    Oliveira, A.3
  • 15
    • 34250171723 scopus 로고    scopus 로고
    • Compressed representations of sequences and full-text indexes
    • doi:10.1145/1240233.1240243
    • Ferragina, P.; Manzini, G.; Mäkinen, V.; Navarro, G. Compressed representations of sequences and full-text indexes. ACM Trans. Algorithms 2007, 3, doi:10.1145/1240233.1240243.
    • (2007) ACM Trans. Algorithms , vol.3
    • Ferragina, P.1    Manzini, G.2    Mäkinen, V.3    Navarro, G.4
  • 16
    • 0037967496 scopus 로고    scopus 로고
    • An analysis of the Burrows-Wheeler transform
    • Manzini, G. An analysis of the Burrows-Wheeler transform. J. ACM 2001, 48, 407-430.
    • (2001) J. ACM , vol.48 , pp. 407-430
    • Manzini, G.1
  • 17
    • 45849125008 scopus 로고    scopus 로고
    • An(other) Entropy-Bounded Compressed Suffix Tree
    • In Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM), Pisa, Italy, 18-20 June 2008
    • Fischer, J.; Mäkinen, V.; Navarro, G. An(other) Entropy-Bounded Compressed Suffix Tree. In Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM), Pisa, Italy, 18-20 June 2008; pp. 152-165.
    • Fischer, J.1    Mäkinen, V.2    Navarro, G.3
  • 18
    • 70349961525 scopus 로고    scopus 로고
    • Faster entropy-bounded compressed suffix trees
    • Fischer, J.; Mäkinen, V.; Navarro, G. Faster entropy-bounded compressed suffix trees. Theory Comput. Sci. 2009, 410, 5354-5364.
    • (2009) Theory Comput. Sci. , vol.410 , pp. 5354-5364
    • Fischer, J.1    Mäkinen, V.2    Navarro, G.3
  • 20
    • 37249088071 scopus 로고    scopus 로고
    • Engineering a Compressed Suffix Tree Implementation
    • In Proceedings of the 6th Workshop on Experimental Algorithms (WEA), Rome, Italy, 6-8 June 2007
    • Välimäki, N.; Gerlach, W.; Dixit, K.; Mäkinen, V. Engineering a Compressed Suffix Tree Implementation. In Proceedings of the 6th Workshop on Experimental Algorithms (WEA), Rome, Italy, 6-8 June 2007; pp. 217-228.
    • Välimäki, N.1    Gerlach, W.2    Dixit, K.3    Mäkinen, V.4
  • 21
    • 84863093621 scopus 로고    scopus 로고
    • Compressed Suffix Trees: Design, Construction, and Applications
    • Ph.D. Thesis, University of Ulm, Ulm, Germany
    • Gog, S. Compressed Suffix Trees: Design, Construction, and Applications. Ph.D. Thesis, University of Ulm, Ulm, Germany, 2011.
    • (2011)
    • Gog, S.1
  • 22
    • 77951686861 scopus 로고    scopus 로고
    • Fully-Functional Succinct Trees
    • In Proceedings of the 21st Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Austin, TX, USA, 17-19 January 2010
    • Sadakane, K.; Navarro, G. Fully-Functional Succinct Trees. In Proceedings of the 21st Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Austin, TX, USA, 17-19 January 2010; pp. 134-149.
    • Sadakane, K.1    Navarro, G.2
  • 23
    • 84880338581 scopus 로고    scopus 로고
    • Succinct Trees in Practice
    • In Proceedings of the 11th Workshop on Algorithm Engineering and Experiments (ALENEX), New York, NY, USA, 3 January 2009
    • Arroyuelo, D.; Ćanovas, R.; Navarro, G.; Sadakane, K. Succinct Trees in Practice. In Proceedings of the 11th Workshop on Algorithm Engineering and Experiments (ALENEX), New York, NY, USA, 3 January 2009; pp. 84-97.
    • Arroyuelo, D.1    Ćanovas, R.2    Navarro, G.3    Sadakane, K.4
  • 24
    • 79960106566 scopus 로고    scopus 로고
    • Self-Indexing Based on LZ77
    • In Proceedings of the 22nd Annual Symposium on Combinatorial Pattern Matching (CPM), Palermo, Italy, 27-29 June 2011
    • Kreft, S.; Navarro, G. Self-Indexing Based on LZ77. In Proceedings of the 22nd Annual Symposium on Combinatorial Pattern Matching (CPM), Palermo, Italy, 27-29 June 2011; pp. 41-54.
    • Kreft, S.1    Navarro, G.2
  • 25
    • 77950788830 scopus 로고    scopus 로고
    • Storage and retrieval of highly repetitive sequence collections
    • Mäkinen, V.; Navarro, G.; Sirén, J.; Välimäki, N. Storage and retrieval of highly repetitive sequence collections. J. Comput. Biol. 2010, 17, 281-308.
    • (2010) J. Comput. Biol. , vol.17 , pp. 281-308
    • Mäkinen, V.1    Navarro, G.2    Sirén, J.3    Välimäki, N.4
  • 26
    • 70349311543 scopus 로고    scopus 로고
    • Self-Indexed Text Compression Using Straight-Line Programs
    • In Proceedings of the 34th International Symposium on Mathematical Foundations of Computer Science (MFCS), Novy Smokovec, Slovakia, 24-28 August 2009
    • Claude, F.; Navarro, G. Self-Indexed Text Compression Using Straight-Line Programs. In Proceedings of the 34th International Symposium on Mathematical Foundations of Computer Science (MFCS), Novy Smokovec, Slovakia, 24-28 August 2009; pp. 235-246.
    • Claude, F.1    Navarro, G.2
  • 27
    • 77956153823 scopus 로고    scopus 로고
    • Compressed q-Gram Indexing for Highly Repetitive Biological Sequences
    • In Proceedings of the 10th IEEE Conference on Bioinformatics and Bioengineering (BIBE), Philadelphia, PA, USA, 31 May-3 June 2010
    • Claude, F.; Fariña, A.; Martínez-Prieto, M.; Navarro, G. Compressed q-Gram Indexing for Highly Repetitive Biological Sequences. In Proceedings of the 10th IEEE Conference on Bioinformatics and Bioengineering (BIBE), Philadelphia, PA, USA, 31 May-3 June 2010; pp. 86-91.
    • Claude, F.1    Fariña, A.2    Martínez-Prieto, M.3    Navarro, G.4
  • 28
    • 78449285802 scopus 로고    scopus 로고
    • CST++
    • In Proceedings of the 17th International Symposium on String Processing and Information Retrieval (SPIRE), Los Cabos, Mexico, 11-13 October 2010
    • Ohlebusch, E.; Fischer, J.; Gog, S. CST++. In Proceedings of the 17th International Symposium on String Processing and Information Retrieval (SPIRE), Los Cabos, Mexico, 11-13 October 2010; pp. 322-333.
    • Ohlebusch, E.1    Fischer, J.2    Gog, S.3
  • 29
    • 84855308006 scopus 로고    scopus 로고
    • Practical Compressed Suffix Trees
    • In Proceedings of the 9th International Symposium on Experimental Algorithms (SEA), Ischia Island, Italy, 20-22 May 2010
    • Ćanovas, R.; Navarro, G. Practical Compressed Suffix Trees. In Proceedings of the 9th International Symposium on Experimental Algorithms (SEA), Ischia Island, Italy, 20-22 May 2010; pp. 94-105.
    • Ćanovas, R.1    Navarro, G.2
  • 30
    • 84867513711 scopus 로고    scopus 로고
    • Compressed Suffix Trees for Repetitive Texts
    • In Proceedings of the 19th International Symposium on String Processing and Information Retrieval (SPIRE), Cartagena, Colombia, 21-25 October 2012
    • Abeliuk, A.; Navarro, G. Compressed Suffix Trees for Repetitive Texts. In Proceedings of the 19th International Symposium on String Processing and Information Retrieval (SPIRE), Cartagena, Colombia, 21-25 October 2012; pp. 30-41.
    • Abeliuk, A.1    Navarro, G.2
  • 31
    • 34147186297 scopus 로고    scopus 로고
    • Compressed full-text indexes
    • doi:10.1145/1216370.1216372
    • Navarro, G.; Mäkinen, V. Compressed full-text indexes. ACM Comput. Surv. 2007, 39, doi:10.1145/1216370.1216372.
    • (2007) ACM Comput. Surv. , vol.39
    • Navarro, G.1    Mäkinen, V.2
  • 33
    • 84947935857 scopus 로고    scopus 로고
    • Tables
    • In Proceedings of the 16th Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS), Hyderabad, India, 18-20 December 1996
    • Munro, I. Tables. In Proceedings of the 16th Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS), Hyderabad, India, 18-20 December 1996; pp. 37-42.
    • Munro, I.1
  • 34
    • 19944392360 scopus 로고    scopus 로고
    • Off-Line dictionary-based compression
    • Larsson, J.; Moffat, A. Off-Line dictionary-based compression. Proc. IEEE 2000, 88, 1722-1732.
    • (2000) Proc. IEEE , vol.88 , pp. 1722-1732
    • Larsson, J.1    Moffat, A.2
  • 35
    • 37849029611 scopus 로고    scopus 로고
    • Compressed Text Indexes with Fast Locate
    • In Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM), London, Canada, 9-11 July 2007
    • González, R.; Navarro, G. Compressed Text Indexes with Fast Locate. In Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM), London, Canada, 9-11 July 2007; pp. 216-227.
    • González, R.1    Navarro, G.2
  • 36
    • 33746044836 scopus 로고    scopus 로고
    • Succinct suffix arrays based on run-length encoding
    • Mäkinen, V.; Navarro, G. Succinct suffix arrays based on run-length encoding. Nord. J. Comput. 2005, 12, 40-66.
    • (2005) Nord. J. Comput. , vol.12 , pp. 40-66
    • Mäkinen, V.1    Navarro, G.2
  • 37
    • 84968909171 scopus 로고    scopus 로고
    • Succinct Indexable Dictionaries with Applications to Encoding k-Ary Trees and Multisets
    • In Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), San Francisco, CA, USA, 6-8 January 2002
    • Raman, R.; Raman, V.; Rao, S. Succinct Indexable Dictionaries with Applications to Encoding k-Ary Trees and Multisets. In Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), San Francisco, CA, USA, 6-8 January 2002; pp. 233-242.
    • Raman, R.1    Raman, V.2    Rao, S.3
  • 38
    • 34547954080 scopus 로고    scopus 로고
    • Practical Entropy-Compressed Rank/Select Dictionary
    • In Proceedings of the 9th Workshop on Algorithm Engineering and Experiments (ALENEX), New Orleans, LA, USA, 6 January 2007
    • Okanohara, D.; Sadakane, K. Practical Entropy-Compressed Rank/Select Dictionary. In Proceedings of the 9th Workshop on Algorithm Engineering and Experiments (ALENEX), New Orleans, LA, USA, 6 January 2007.
    • Okanohara, D.1    Sadakane, K.2
  • 39
    • 33845514938 scopus 로고    scopus 로고
    • Practical Implementation of Rank and Select Queries
    • In Proceedings of the posters 4th Workshop on Experimental Algorithms (WEA), Santorini Island, Greece, 10-13 May 2005
    • González, R.; Grabowski, S.; Mäkinen, V.; Navarro, G. Practical Implementation of Rank and Select Queries. In Proceedings of the posters 4th Workshop on Experimental Algorithms (WEA), Santorini Island, Greece, 10-13 May 2005; pp. 27-38.
    • González, R.1    Grabowski, S.2    Mäkinen, V.3    Navarro, G.4
  • 40
    • 85041120916 scopus 로고    scopus 로고
    • Practical Rank/Select Queries over Arbitrary Sequences
    • In Proceedings of the 15th International Symposium on String Processing and Information Retrieval (SPIRE), Melbourne Australia, 10-12 November 2008
    • Claude, F.; Navarro, G. Practical Rank/Select Queries over Arbitrary Sequences. In Proceedings of the 15th International Symposium on String Processing and Information Retrieval (SPIRE), Melbourne Australia, 10-12 November 2008; pp. 176-187.
    • Claude, F.1    Navarro, G.2
  • 41
    • 58549114255 scopus 로고    scopus 로고
    • Space-Time Tradeoffs for Longest-Common-Prefix Array Computation
    • In Proceedings of the 19th International Symposium on Algorithms and Computation (ISAAC), Gold Coast, Australia, 15-17 December 2008
    • Puglisi, S.; Turpin, A. Space-Time Tradeoffs for Longest-Common-Prefix Array Computation. In Proceedings of the 19th International Symposium on Algorithms and Computation (ISAAC), Gold Coast, Australia, 15-17 December 2008; pp. 124-135.
    • Puglisi, S.1    Turpin, A.2
  • 42
    • 70350648554 scopus 로고    scopus 로고
    • Permuted Longest-Common-Prefix Array
    • In Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching (CPM), Lille, France, 22-24 June 2009
    • Kärkkäinen, J.; Manzini, G.; Puglisi, S. Permuted Longest-Common-Prefix Array. In Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching (CPM), Lille, France, 22-24 June 2009; pp. 181-192.
    • Kärkkäinen, J.1    Manzini, G.2    Puglisi, S.3
  • 43
    • 70350666481 scopus 로고    scopus 로고
    • Directly Addressable Variable-length Codes
    • In Proceedings of the 16th International Symposium on String Processing and Information Retrieval (SPIRE), Saariselk, Finland, 25-27 August 2009
    • Brisaboa, N.; Ladra, S.; Navarro, G. Directly Addressable Variable-length Codes. In Proceedings of the 16th International Symposium on String Processing and Information Retrieval (SPIRE), Saariselk, Finland, 25-27 August 2009; pp. 122-130.
    • Brisaboa, N.1    Ladra, S.2    Navarro, G.3
  • 44
    • 84880411472 scopus 로고    scopus 로고
    • Pizza & Chili Corpus
    • Available online, (accessed on 20 May 2013)
    • Pizza & Chili Corpus. Available online: http://pizzachili.dcc.uchile.cl (accessed on 20 May 2013).
  • 45
    • 33751016062 scopus 로고    scopus 로고
    • A simple optimal representation for balanced parentheses
    • Geary, R.; Rahman, N.; Raman, R.; Raman, V. A simple optimal representation for balanced parentheses. Theory Comput. Sci. 2006, 368, 231-246.
    • (2006) Theory Comput. Sci. , vol.368 , pp. 231-246
    • Geary, R.1    Rahman, N.2    Raman, R.3    Raman, V.4
  • 46
    • 79957456930 scopus 로고    scopus 로고
    • Space-Efficient preprocessing schemes for range minimum queries on static arrays
    • Fischer, J.; Heun, V. Space-Efficient preprocessing schemes for range minimum queries on static arrays. SIAM J. Comput. 2011, 40, 465-492.
    • (2011) SIAM J. Comput. , vol.40 , pp. 465-492
    • Fischer, J.1    Heun, V.2
  • 47
    • 84881036469 scopus 로고    scopus 로고
    • Faster Compact Top-k Document Retrieval
    • In Proceedings of the 23rd Data Compression Conference (DCC), Snowbird, UT, USA, 20 March 2013
    • Konow, R.; Navarro, G. Faster Compact Top-k Document Retrieval. In Proceedings of the 23rd Data Compression Conference (DCC), Snowbird, UT, USA, 20 March 2013; pp. 351-360.
    • Konow, R.1    Navarro, G.2
  • 48
    • 18544376055 scopus 로고    scopus 로고
    • A fully linear-time approximation algorithm for grammar-based compression
    • Sakamoto, H. A fully linear-time approximation algorithm for grammar-based compression. J. Discret. Algorithms 2005, 3, 416-430.
    • (2005) J. Discret. Algorithms , vol.3 , pp. 416-430
    • Sakamoto, H.1
  • 49
    • 84880414245 scopus 로고    scopus 로고
    • Pizza&Chili Repetitive Corpus
    • Available online:(accessed on 20 May 2013)
    • Pizza&Chili Repetitive Corpus. Available online: http://pizzachili.dcc.uchile.cl/repcorpus (accessed on 20 May 2013).
  • 50
    • 84880443002 scopus 로고    scopus 로고
    • Software Page of Gonzalo Navarro
    • Available online:(accessed on 20 May 2013)
    • Software Page of Gonzalo Navarro. Available online: http://www.dcc.uchile.cl/gnavarro/software (accessed on 20 May 2013).
  • 51
    • 84880411472 scopus 로고    scopus 로고
    • Pizza & Chili Corpus
    • Available online:(accessed on 20 May 2013)
    • Pizza & Chili Corpus. Available online: http://pizzachili.dcc.uchile.cl/cst (accessed on 20 May 2013).


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