Linear Time Suffix Array Construction Using D-Critical Substrings
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
A Linear-Time Burrows-Wheeler Transform Using Induced Sorting
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Lempel-Ziv factorization revisited
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
WADS'11 Proceedings of the 12th international conference on Algorithms and data structures
Computing the longest common prefix array based on the burrows-wheeler transform
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
An index structure for spaced seed search
ISAAC'11 Proceedings of the 22nd international conference on Algorithms and Computation
Improving tweet stream classification by detecting changes in word probability
SIGIR '12 Proceedings of the 35th international ACM SIGIR conference on Research and development in information retrieval
Parallel suffix array construction for shared memory architectures
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
Computing the longest common prefix array based on the Burrows-Wheeler transform
Journal of Discrete Algorithms
Trends in suffix sorting: a survey of low memory algorithms
ACSC '12 Proceedings of the Thirty-fifth Australasian Computer Science Conference - Volume 122
Brief announcement: truly parallel burrows-wheeler compression and decompression
Proceedings of the twenty-fifth annual ACM symposium on Parallelism in algorithms and architectures
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We present a linear time and space suffix array (SA) construction algorithm called the SA-IS algorithm.The SA-IS algorithm is novel because of the LMS-substrings used for the problem reduction and the pure induced-sorting (specially coined for this algorithm)used to propagate the order of suffixes as well as that of LMS-substrings, which makes the algorithm almost purely relying on induced sorting at both its crucial steps.The pure induced-sorting renders the algorithm an elegant design and in turn a surprisingly compact implementation which consists of less than 100 lines of C code.The experimental results demonstrate that this newly proposed algorithm yields noticeably better time and space efficiencies than all the currently published linear time algorithms for SA construction.