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
Algorithms on strings, trees, and sequences: computer science and computational biology
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
An analysis of the Burrows—Wheeler transform
Journal of the ACM (JACM)
Succinct indexable dictionaries with applications to encoding k-ary trees and multisets
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
Proceedings of the 16th Conference on Foundations of Software Technology and Theoretical Computer Science
Succinct suffix arrays based on run-length encoding
Nordic Journal of Computing
ACM Computing Surveys (CSUR)
Compressed Suffix Trees with Full Functionality
Theory of Computing Systems
Compressed Text Indexes with Fast Locate
CPM '07 Proceedings of the 18th annual symposium on Combinatorial Pattern Matching
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
Compressed text indexes: From theory to practice
Journal of Experimental Algorithmics (JEA)
Self-indexed Text Compression Using Straight-Line Programs
MFCS '09 Proceedings of the 34th International Symposium on Mathematical Foundations of Computer Science 2009
Directly Addressable Variable-Length Codes
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Faster entropy-bounded compressed suffix trees
Theoretical Computer Science
Information Processing Letters
Compressed q-Gram Indexing for Highly Repetitive Biological Sequences
BIBE '10 Proceedings of the 2010 IEEE International Conference on Bioinformatics and Bioengineering
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
ACM Transactions on Algorithms (TALG)
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Practical compressed suffix trees
SEA'10 Proceedings of the 9th international conference on Experimental Algorithms
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We design a new compressed suffix tree specifically tailored to highly repetitive text collections. This is particularly useful for sequence analysis on large collections of genomes of the close species. We build on an existing compressed suffix tree that applies statistical compression, and modify it so that it works on the grammar-compressed version of the longest common prefix array, whose differential version inherits much of the repetitiveness of the text.