New indices for text: PAT Trees and PAT arrays
Information retrieval
Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
Algorithms on strings, trees, and sequences: computer science and computational biology
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Fast algorithms for sorting and searching strings
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing
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Software—Practice & Experience
An experimental study of an opportunistic index
SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
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SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
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WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
LATIN '00 Proceedings of the 4th Latin American Symposium on Theoretical Informatics
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SPIRE 2002 Proceedings of the 9th International Symposium on String Processing and Information Retrieval
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CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
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CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
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FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
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FOCS '00 Proceedings of the 41st Annual Symposium on Foundations of Computer Science
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CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
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CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
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ICALP'03 Proceedings of the 30th international conference on Automata, languages and programming
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The VLDB Journal — The International Journal on Very Large Data Bases
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ICDM '05 Proceedings of the Fifth IEEE International Conference on Data Mining
Software—Practice & Experience
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Information Processing Letters
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ICML '06 Proceedings of the 23rd international conference on Machine learning
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ADC '06 Proceedings of the 17th Australasian Database Conference - Volume 49
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ACM Transactions on Algorithms (TALG)
ACM Computing Surveys (CSUR)
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Theoretical Computer Science
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Journal of the ACM (JACM)
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Journal of Parallel and Distributed Computing
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Information Processing Letters
A taxonomy of suffix array construction algorithms
ACM Computing Surveys (CSUR)
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Journal of Experimental Algorithmics (JEA)
Efficient token based clone detection with flexible tokenization
Proceedings of the the 6th joint meeting of the European software engineering conference and the ACM SIGSOFT symposium on The foundations of software engineering
Efficient token based clone detection with flexible tokenization
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The affix array data structure and its applications to RNA secondary structure analysis
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Information Processing Letters
International Journal of Bioinformatics Research and Applications
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Proceedings of the 2008 ACM SIGMOD international conference on Management of data
Counting suffix arrays and strings
Theoretical Computer Science
Fast profile matching algorithms – A survey
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The Journal of Machine Learning Research
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Data Mining and Knowledge Discovery
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CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
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ICDM '08 Proceedings of the 8th industrial conference on Advances in Data Mining: Medical Applications, E-Commerce, Marketing, and Theoretical Aspects
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ESA '08 Proceedings of the 16th annual European symposium on Algorithms
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WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
On-line construction of compact suffix vectors and maximal repeats
Theoretical Computer Science
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Proceedings of the 17th ACM conference on Information and knowledge management
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SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
Efficient Algorithms for the Computational Design of Optimal Tiling Arrays
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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PADL '09 Proceedings of the 11th International Symposium on Practical Aspects of Declarative Languages
PSISA: an algorithm for indexing and searching protein structure using suffix arrays
ICCOMP'08 Proceedings of the 12th WSEAS international conference on Computers
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DASFAA '09 Proceedings of the 14th International Conference on Database Systems for Advanced Applications
Proceedings of the 2008 conference on ECAI 2008: 18th European Conference on Artificial Intelligence
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SEA '09 Proceedings of the 8th International Symposium on Experimental Algorithms
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CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Transformation of Suffix Arrays into Suffix Trees on the MPI Environment
RSFDGrC '07 Proceedings of the 11th International Conference on Rough Sets, Fuzzy Sets, Data Mining and Granular Computing
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Journal of Experimental Algorithmics (JEA)
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SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
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Computational Statistics & Data Analysis
Information Processing Letters
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Information and Software Technology
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BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
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WEA'07 Proceedings of the 6th international conference on Experimental algorithms
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ICIP'09 Proceedings of the 16th IEEE international conference on Image processing
Maximal phrases based analysis for prototyping online discussion forums postings
AdaptLRTtoND '09 Proceedings of the Workshop on Adaptation of Language Resources and Technology to New Domains
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ICGI'10 Proceedings of the 10th international colloquium conference on Grammatical inference: theoretical results and applications
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DS'10 Proceedings of the 13th international conference on Discovery science
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
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SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
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SEAL'10 Proceedings of the 8th international conference on Simulated evolution and learning
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MFCS'12 Proceedings of the 37th international conference on Mathematical Foundations of Computer Science
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EuroMPI'12 Proceedings of the 19th European conference on Recent Advances in the Message Passing Interface
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Machine Translation
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Science of Computer Programming
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Electronic Notes in Theoretical Computer Science (ENTCS)
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The suffix tree is one of the most important data structures in string processing and comparative genomics. However, the space consumption of the suffix tree is a bottleneck in large scale applications such as genome analysis. In this article, we will overcome-this obstacle. We will show how every algorithm that uses a suffix tree as data structure can systematically be replaced with an algorithm that uses an enhanced suffix array and solves the same problem in the same time complexity. The generic name enhanced suffix array stands for data structures consisting of the suffix array and additional tables. Our new algorithms are not only more space efficient than previous ones, but they are also faster and easier to implement.