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
Fast algorithms for sorting and searching strings
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Reducing the space requirement of suffix trees
Software—Practice & Experience
Simple and flexible detection of contiguous repeats using a suffix tree
Theoretical Computer Science
Optimal Exact Strring Matching Based on Suffix Arrays
SPIRE 2002 Proceedings of the 9th International Symposium on String Processing and Information Retrieval
Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Finding Maximal Repetitions in a Word in Linear Time
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
Optimal Exact Strring Matching Based on Suffix Arrays
SPIRE 2002 Proceedings of the 9th International Symposium on String Processing and Information Retrieval
Fast and Sensitive Probe Selection for DNA Chips Using Jumps in Matching Statistics
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
EMAGEN: an efficient approach to multiple whole genome alignment
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
When indexing equals compression: experiments with compressing suffix arrays and applications
SODA '04 Proceedings of the fifteenth annual ACM-SIAM symposium on Discrete algorithms
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
An O(N^2) Algorithm for Discovering Optimal Boolean Pattern Pairs
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Detecting higher-level similarity patterns in programs
Proceedings of the 10th European software engineering conference held jointly with 13th ACM SIGSOFT international symposium on Foundations of software engineering
Software—Practice & Experience
Longest repeats with a block of k don't cares
Theoretical Computer Science
Scalable parallel suffix array construction
Parallel Computing
The affix array data structure and its applications to RNA secondary structure analysis
Theoretical Computer Science
Better external memory suffix array construction
Journal of Experimental Algorithmics (JEA)
An Alignment-Free Distance Measure for Closely Related Genomes
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
A Simple Algorithm for Finding Exact Common Repeats
IEICE - Transactions on Information and Systems
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
Fast lightweight suffix array construction and checking
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Space efficient linear time construction of suffix arrays
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Simple linear work suffix array construction
ICALP'03 Proceedings of the 30th international conference on Automata, languages and programming
The solution space of genome sequence alignment and LIS graph decomposition
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Scalable parallel suffix array construction
EuroPVM/MPI'06 Proceedings of the 13th European PVM/MPI User's Group conference on Recent advances in parallel virtual machine and message passing interface
Linear time algorithm for the generalised longest common repeat problem
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
Efficient distributed computation of maximal exact matches
EuroMPI'12 Proceedings of the 19th European conference on Recent Advances in the Message Passing Interface
A Compressed Suffix Tree Based Implementation With Low Peak Memory Usage
Electronic Notes in Theoretical Computer Science (ENTCS)
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In large scale applications as computational genome analysis, the space requirement of the suffix tree is a severe drawback. In this paper, we present a uniform framework that enables us to systematically replace every string processing algorithm that is based on a bottomup traversal of a suffix tree by a corresponding algorithm based on an enhanced suffix array (a suffix array enhanced with the lcp-table). In this framework, we will show how maximal, supermaximal, and tandem repeats, as well as maximal unique matches can be efficiently computed. Because enhanced suffix arrays require much less space than suffix trees, very large genomes can now be indexed and analyzed, a task which was not feasible before. Experimental results demonstrate that our programs require not only less space but also much less time than other programs developed for the same tasks.