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On-line Construction of Two-Dimensional Suffix Trees

Raffaele Giancarlo, Daniela Guaiana
1999 Journal of Complexity  
To the best of our knowledge, our technique is the first one that effectively addresses problems related to the on-line construction of two-dimensional suffix trees.  ...  the two-dimensional analog of the suffix tree of a string; (b) simple algorithms implementing primitive operations for LZ1type on-line lossless image compression methods.  ...  Moreover, our gratitude goes to the referees for their competent reviews and most valuable comments that greatly helped the presentation of our ideas.  ... 
doi:10.1006/jcom.1998.0495 fatcat:zsyvhgxjifgsrnhks5ic6lwr3y

A Novel Indexing Method for Efficient Sequence Matching in Large DNA Database Environment [chapter]

Jung-Im Won, Jee-Hee Yoon, Sanghyun Park, Sang-Wook Kim
2005 Lecture Notes in Computer Science  
The results reveal that the proposed approach, which requires smaller storage space, can be a few orders of magnitude faster than the suffix tree.  ...  In this paper, we first point out the problems of the suffix tree, an index structure widely-used for DNA sequence matching, in the respects of the storage overhead, search performance, and difficulty  ...  Since the suffixes are the inputs to the trie construction algorithm, the resultant tree has the properties of suffix tries [17] .  ... 
doi:10.1007/11430919_26 fatcat:cmdoinkgkvf2vor2ns3k6c6i2y

An efficient approach for sequence matching in large DNA databases

Jung-Im Won, Sanghyun Park, Jee-Hee Yoon, Sang-Wook Kim
2006 Journal of information science  
The results reveal that the proposed approach, which requires smaller storage space, can be a few orders of magnitude faster than the suffix tree.  ...  In this paper, we first point out the problems of the suffix tree, an index structure widely-used for DNA sequence matching, in respect of storage overhead, search performance, and difficulty in seamless  ...  [12] suggested an algorithm for constructing a disk-based suffix tree on huge DNA databases, and proposed an approximate subsequence matching algorithm that exploits the suffix tree.  ... 
doi:10.1177/0165551506059229 fatcat:l2ea2b57jjd5xdztqhx3tjef6m

A prototype for multiple whole genome alignment

J.S. Deogun, Fangrui Ma, Jingyi Yang, A. Benson
2003 36th Annual Hawaii International Conference on System Sciences, 2003. Proceedings of the  
To develop our algorithm, we have to solve several problems including decomposition of genomes with a suffix tree, finding an LIS for multiple MUM sequences, and iterative pairwise multiple sequence alignment  ...  One of the motivating application is the problem of finding maximum set of conserved regions in closely related microorganisms. *  ...  A string of length n has a total of n suffixes, one starting at each position in the string. To construct the suffix tree, we start with a tree consisting of one node as a root.  ... 
doi:10.1109/hicss.2003.1174803 dblp:conf/hicss/DeogunMYB03 fatcat:n522thc5ynfozms6nu7lspl3be

An Gray Box for Visualizing Instruction Sequence Based on Improved Suffix Tree

Donglin Wang, Jiandong Fang
2020 IEEE Access  
Adhering to the idea of latest researches, our paper improves the original suffix tree and use the improved suffix tree as a mathematical models to analyse and visualize the internal logic of instructions  ...  INDEX TERMS Gray box, reverse engineering, suffix tree, visualize, instruction preprocess.  ...  CONSTRUCTING TIME CONSUME In the abstract of paper On-line construction of suffix trees [10] , Ukkonen said ''Regardless of its quadratic worst case this latter algorithm can be a good practical method  ... 
doi:10.1109/access.2020.3009990 fatcat:p44f6uvyyvex7dld5cpuwp3s2u

Discovering 3D Protein Structures for Optimal Structure Alignment [chapter]

Tomá Novosád, Václav Snáel, Ajith Abraham, Jack Y. Yang
2013 Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics  
Various suffix tree construction algorithms can be found in [10] (a good book on suffix tree construction algorithms in general).  ...  Inserting All Main Chains into the Suffix Tree At this stage of the algorithm, we construct a generalized suffix tree of all encoded main chains.  ... 
doi:10.1002/9781118567869.ch14 fatcat:xikkcrzbwba37pegbib43qhu3m

Prosima: Protein similarity algorithm

Tomas Novosad, Vaclav Snasel, Ajith Abraham, Jack Y Yang
2009 2009 World Congress on Nature & Biologically Inspired Computing (NaBIC)  
In this article we present a novel algorithm for measuring protein similarity based on their three dimensional structure (protein tertiary structure).  ...  The PROSIMA algorithm using suffix tress for discovering common parts of main-chains of all proteins appearing in current NCSB Protein Data Bank (PDB).  ...  Inserting All Main Chains into the Suffix Tree In this stage of the algorithm we will be constructing a generalized suffix tree of all encoded main chains.  ... 
doi:10.1109/nabic.2009.5393605 dblp:conf/nabic/NovosadSAY09 fatcat:rk6dbnhihnh7lgklqdwqu6c77e

Detecting Duplications in Sequence Diagrams Based on Suffix Trees

Hui Liu, Zhiyi Ma, Lu Zhang, Weizhong Shao
2006 2006 13th Asia Pacific Software Engineering Conference (APSEC'06)  
With special preprocessing, we convert 2-dimensional sequence diagrams into a 1-dimensional array. Then we construct a suffix tree of the array.  ...  We revise the traditional construction algorithm of suffix trees by proposing a special algorithm to detect common prefixes of suffixes.  ...  The focus of suffix tree based approaches is the construction of the suffix trees. The core of the construction is an algorithm to detect the longest common prefixes of any pair of suffixes.  ... 
doi:10.1109/apsec.2006.32 dblp:conf/apsec/LiuMZS06 fatcat:pxejjzupcndo7ix4ih4gqkg3ci

YAPS: Yet Another Protein Similarity

Tomáš Novosád, Václav Snášel, Ajith Abraham, Jack Y. Yang
2009 2009 International Conference of Soft Computing and Pattern Recognition  
Our new method deals with suffix trees and classical information retrieval tasks, such as the vector space model, using tf-idf term weighing schema or using various types of similarity measures.  ...  In this article we present a novel method for measuring protein similarity based on their tertiary structure.  ...  Inserting All Main Chains into the Suffix Tree In this stage of the algorithm we will be constructing a generalized suffix tree of all encoded main chains.  ... 
doi:10.1109/socpar.2009.101 dblp:conf/socpar/NovosadSAY09 fatcat:hdtefhzfx5gyhppqp3azbbexuq

Optimizing data intensive GPGPU computations for DNA sequence alignment

Cole Trapnell, Michael C. Schatz
2009 Parallel Computing  
MUMmerGPU uses highly-parallel commodity graphics processing units (GPU) to accelerate the data-intensive computation of aligning next generation DNA sequence data to a reference sequence for use in diverse  ...  MUMmerGPU 2.0 features a new stackless depth-first-search print kernel and is 13Â faster than the serial CPU version of the alignment code and nearly 4Â faster in total computation time than MUMmerGPU  ...  Acknowledgements The authors would like to thank Steven Salzberg from the University of Maryland for helpful comments on the manuscript.  ... 
doi:10.1016/j.parco.2009.05.002 pmid:20161021 pmcid:PMC2749273 fatcat:dy5mcyhqanayvafxrrqzq7njpm

Managing Unbounded-Length Keys in Comparison-Driven Data Structures with Applications to On-Line Indexing [article]

Amihood Amir and Gianni Franceschini and Roberto Grossi and Tsvi Kopelowitz and Moshe Lewenstein and Noa Lewenstein
2013 arXiv   pre-print
Searching for a pattern of length m in the resulting suffix tree takes O((m |Σ|, m + n) + tocc) time, where tocc is the number of occurrences of the pattern.  ...  Using the proposed technique, online suffix tree can be constructed in worst case time O( n) per input symbol (as opposed to amortized O( n) time per symbol, achieved by previously known algorithms).  ...  Finding the entry point We now proceed to the online construction of the suffix tree.  ... 
arXiv:1306.0406v1 fatcat:sczacv2x65csvjgoz2v2okntuu

The S 2-Tree: An Index Structure for Subsequence Matching of Spatial Objects [chapter]

Haixun Wang, Chang-Shing Perng
2001 Lecture Notes in Computer Science  
We present the S 2 -Tree, an indexing method for subsequence matching of spatial objects.  ...  Moreover, it supports queries such as "what is the longest common pattern of the two time series?", which previous subsequence matching algorithms find difficult to solve efficiently.  ...  McCreight's algorithm builds a suffix tree in linear time and is space efficient [1] . Ukkonen [2] developed a linear-time, on-line suffix tree construction algorithm.  ... 
doi:10.1007/3-540-45357-1_34 fatcat:m43dp4cfajhudl2oyshdsnunvm

Managing Unbounded-Length Keys in Comparison-Driven Data Structures with Applications to Online Indexing

Amihood Amir, Gianni Franceschini, Roberto Grossi, Tsvi Kopelowitz, Moshe Lewenstein, Noa Lewenstein
2014 SIAM journal on computing (Print)  
Using the proposed technique, online suffix tree construction can be done in worst case time O(log n) per input symbol (as opposed to amortized O(log n) time per symbol, achieved by previously known algorithms  ...  Searching for a pattern of length m in the resulting suffix tree takes O(min(m log |Σ|, m + log n) + tocc) time, where tocc is the number of occurrences of the pattern.  ...  Finding the entry point We now proceed to the online construction of the suffix tree.  ... 
doi:10.1137/110836377 fatcat:bwv6mhk6dvatbc4ty6szymlkli

A General Model for Authenticated Data Structures

Charles Martel, Glen Nuckolls, Premkumar Devanbu, Michael Gertz, April Kwong, Stuart G. Stubblebine
2004 Algorithmica  
We demonstrate how this approach easily captures existing work on simple structures such as binary trees, multi-dimensional range trees, tries, and skip lists.  ...  Going further, we also use Search DAGs to produce and prove the security of authenticated versions of two complex data models for efficient multi-dimensional range searches.  ...  A two dimensional MDRT (for N points (x i , y i )) consists of a base tree which is a binary search tree (BST) whose leaves are the points sorted by x-coordinate.  ... 
doi:10.1007/s00453-003-1076-8 fatcat:mihn67x52jd2nhtyuoriw5aj3a

Page 510 of Mathematical Reviews Vol. , Issue 2002A [page]

2002 Mathematical Reviews  
The authors introduce a modification to the k-d tree (k- dimensional binary search tree). Their squarish k-d tree uses 68 COMPUTER SCIENCE 510 a different procedure for on-line insertion.  ...  As a result, the expected time behavior of lower-dimensional partial match queries is the same as for perfectly balanced complete k-d trees on n nodes.  ... 
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