A. Andersson and S. Nilsson. Efficient Implementation of Suffix Trees. Software--Practice and Experience (SPE), 25(2):129--141, 1995. Home/Search Document Details and Download
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The Burrows-Wheeler Transform: Theory and Practice - Manzini (1999) (Correct)
....before, larger blocks usually yield better compression) For this reason suffix tree algorithms have not been commonly used for computing the BWT. Recently this state of affair has begun to change. A currently active area of research is the development of compact representations of suffix trees [1, 17]. For example, one the algorithms in [17] builds a suffix tree using 20 bytes per input symbol in the worst case and 10 bytes per input symbol on average for real life files. The use of these space economical suffix tree construction algorithms for the BWT has been discussed in [4] A data ....
A. Andersson and S. Nilsson. Efficient implementation of suffix trees. Software --- Practice and Experience, 25(2):129--141, 1995.
PJama Stores and Suffix Tree Indexing for Bioinformatics.. - Hunt (2000) (Correct)
....non empty substring, and at each branching node the starting letters of the outgoing edges are different, so that each path from the root to a leaf spells the suffix that starts at the sequence position held in the leaf. Suffix tree optimisations, and efficient disk access schemes are discussed in [2, 16], and recent uses of suffix trees in biological sequence analysis are reviewed in [17] Our implementation of suffix trees is not optimised for space, and incurs overheads resulting from the use of object orientation and persistence. We focus on the viability of object oriented tree construction ....
A. Andersson and S. Nilsson. Efficient Implementation of Suffix Trees. Software Practice and Experience, 25(2):129--141, Feb. 1995. 14 http://www.w3c.org/Jigsaw
Persistent Suffix Trees and Suffix Binary Search Trees as .. - Hunt, Irving, Atkinson (2000) (Correct)
....T T A T A A A C A A 1 3 C 5 2 9 8 T T 7 6 4 root A C A T C T T A 1 2 3 4 5 6 7 8 9 Figure 1: The suffix tree for ACATCTTA with search on substring T. The string length n = 9, query length k = 1, and the number of occurrences m = 3. schemes are discussed in [2, 27], and recent uses of suffix trees in biological sequence analysis are reviewed in [31] Suffix trees are used in string searching and repeat identification. In Figure 1 an example search for the substring T of length 1 is traced. The search starts at the root and traces the substring along the ....
Arne Andersson and Stefan Nilsson. Efficient implementation of suffix trees. Software Practice and Experience, 25(2):129--141, 1995.
The Suffix Binary Search Tree and Suffix AVL Tree - Irving, Love (2000) (Correct)
.... Suffix trees (ST in the tables) were constructed using a tight implementation of Ukkonen s algorithm with the children of a node organised as a linked list [10] while recognising that this may be neither the fastest suffix tree construction algorithm nor the most economical representation [2, 7]. The suffix array implementation (SA in the tables) was the one used in the experiments of Manber and Myers 4 [8] Four variants of the SBST were included, namely ffl SBSTS the standard construction algorithm; ffl SBSTA standard construction with AVL balancing; ffl SBSTR the ....
A. Andersson and S. Nilsson. Efficient implementation of suffix trees. Software - Practice and Experience, 25(1):129 -- 141, 1995.
Second Year Report - Love (1999) (Correct)
.... on line property of scanning the string symbol by symbol, from left to right, in such a way that, after each iteration, the suffix tree for the processed portion has been constructed. For these reasons, Ukkonen s algorithm has come to be the most commonly used in practice. Andersson and Nilsson [4] have used several methods of compression to build a simple, compact, and efficient representation of a suffix tree. They claim 3 12 11 8 1 4 6 9 2 5 7 10 3 1 2 3 5 6 7 8 9 10 11 12 4 Figure 1.1: A sorted array of the suffixes of abracadabra that their representation will prove to be ....
A. Andersson and S. Nilsson. Efficient implementation of suffix trees. Software - Practice and Experience, 25(1):129 -- 141, 1995.
The Suffix Binary Search Tree and Suffix AVL Tree - Irving, Love (2000) (Correct)
....the results obtained for the various construction algorithms using strings of 1,000,000 characters. Suffix trees (ST in the table) were constructed using a tight implementation of Ukkonen s algorithm [9] while recognising that, with substantial effort, faster implementations may be possible [2]. The suffix array implementation (SA in the table) was that used in [7] Four variants of the suffix BST were included, namely ffl SBSTS the standard construction algorithm; ffl SBSTA standard construction with AVL balancing; ffl SBSTR the refined construction algorithm; 30 ....
A. Andersson and S. Nilsson. Efficient implementation of suffix trees. Software - Practice and Experience, 25(1):129 -- 141, 1995.
Implementing a Dynamic Compressed Trie - Nilsson, Tikkanen (1998) (4 citations) Self-citation (Nilsson) (Correct)
....again, the idea is simple: subtries that are complete (all children are present) are compressed, and this compression is performed top down, see Figure 1c. Previously this technique has only been used in static data structures, where efficient insertion and deletion operations are not provided [4]. The level compressed trie, LC trie, has proved to be of interest both in theory and practice. It is known that the average expected depth of an LC trie is O(log log n) for data from a large class of distributions [3] This should be compared to the logarithmic depth of uncompressed and path ....
....in Section 2 would give memory usage very similar to the treap. There are many other possible further optimizations. For data with a very skewed distribution such as the English text, one might introduce a preprocessing step, where the strings are compressed, resulting in a more even distribution [4]. For example, order preserving Huffman coding could be used. 5. Conclusions and Further Research For both integers and text strings, the average depth of the LPC trie is much less than that of the balanced binary search tree, resulting in better search times. In our experiments, the time to ....
A. Andersson, S. Nilsson. Efficient implementation of suffix trees. Software -- Practice and Experience, 25(2):129--141, 1995.
Practical Suffix Tree Construction - Tata, Hankins, Patel (2004) (Correct)
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A. Andersson and S. Nilsson. Efficient Implementation of Suffix Trees. Software--Practice and Experience (SPE), 25(2):129--141, 1995.
Practical Suffix Tree Construction - Tata, Hankins, Patel (2004) (Correct)
No context found.
A. Andersson and S. Nilsson. Efficient Implementation of Suffix Trees. Software--Practice and Experience (SPE), 25(2):129--141, 1995.
Database indexing for large DNA and protein sequence.. - Hunt, Atkinson, Irving (2002) (Correct)
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A. Andersson, S. Nilsson. Efficient implementation of suffix trees. Software Pract Exp 25(2):129--141, 1995
Compressed Suffix Arrays and Suffix Trees with Applications.. - Grossi, Vitter (2000) (8 citations) (Correct)
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A. Andersson and S. Nilsson. Efficient implementation of suffix trees. Software Practice and Experience, 25(2):129--141, Feb. 1995.
Structures of String Matching and Data Compression - Larsson (1999) (10 citations) (Correct)
No context found.
Arne Andersson and Stefan Nilsson, Efficient implementation of suffix trees, Software -- Practice and Experience 25 (1995), no 2, 129--141.
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