Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
A taxonomy of suffix array construction algorithms
ACM Computing Surveys (CSUR)
Better external memory suffix array construction
Journal of Experimental Algorithmics (JEA)
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
A Linear-Time Burrows-Wheeler Transform Using Induced Sorting
SPIRE '09 Proceedings of the 16th International Symposium on String Processing and Information Retrieval
Linear-time construction of suffix arrays
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
Lightweight BWT construction for very large string collections
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
Two Efficient Algorithms for Linear Time Suffix Array Construction
IEEE Transactions on Computers
Lightweight Data Indexing and Compression in External Memory
Algorithmica - Special Issue: Theoretical Informatics
Trends in suffix sorting: a survey of low memory algorithms
ACSC '12 Proceedings of the Thirty-fifth Australasian Computer Science Conference - Volume 122
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We present a new suffix array construction algorithm that aims to build, in external memory, the suffix array for an input string of length n measured in the magnitude of tens of Giga characters over a constant or integer alphabet. The core of this algorithm is adapted from the framework of the original internal memory SA-DS algorithm that samples fixed-size d-critical substrings. This new external-memory algorithm, called EM-SA-DS, uses novel cache data structures to construct a suffix array in a sequential scanning manner with good data spatial locality: data is read from or written to disk sequentially. On the assumed external-memory model with RAM capacity Ω((nB)0.5), disk capacity O(n), and size of each I/O block B, all measured in log n-bit words, the I/O complexity of EM-SA-DS is O(n/B). This work provides a general cache-based solution that could be further exploited to develop external-memory solutions for other suffix-array-related problems, for example, computing the longest-common-prefix array, using a modern personal computer with a typical memory configuration of 4GB RAM and a single disk.