
This Article  
 
Share  
Bibliographic References  
Add to:  
Digg Furl Spurl Blink Simpy Del.icio.us Y!MyWeb  
Search  
 
ASCII Text  x  
ChingFung Cheung, Jeffrey Xu Yu, Hongjun Lu, "Constructing Suffix Tree for Gigabyte Sequences with Megabyte Memory," IEEE Transactions on Knowledge and Data Engineering, vol. 17, no. 1, pp. 90105, January, 2005.  
BibTex  x  
@article{ 10.1109/TKDE.2005.3, author = {ChingFung Cheung and Jeffrey Xu Yu and Hongjun Lu}, title = {Constructing Suffix Tree for Gigabyte Sequences with Megabyte Memory}, journal ={IEEE Transactions on Knowledge and Data Engineering}, volume = {17}, number = {1}, issn = {10414347}, year = {2005}, pages = {90105}, doi = {http://doi.ieeecomputersociety.org/10.1109/TKDE.2005.3}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE Transactions on Knowledge and Data Engineering TI  Constructing Suffix Tree for Gigabyte Sequences with Megabyte Memory IS  1 SN  10414347 SP90 EP105 EPD  90105 A1  ChingFung Cheung, A1  Jeffrey Xu Yu, A1  Hongjun Lu, PY  2005 KW  Biological sequences KW  database index KW  and suffix tree. VL  17 JA  IEEE Transactions on Knowledge and Data Engineering ER   
[1] R. BaezaYates and G. Navarro, “A Hybrid Indexing Method for Approximate String Matching,” J. Discrete Algorithms, 2000.
[2] M. Bender and M. FarachColton, “The LCA Problem Revisited,” Proc. Fourth Am. Symp. Theoretical Informatics, pp. 8894, 2000.
[3] P. Bieganski, “Genetic Sequence Data Retrieval and Manipulation Based on Generalized Suffix Trees,” PhD thesis, Univ. of Minnesota, 1995.
[4] E. Coffman, M. Garey, and D. Johnson, Approximation Algorithms for Bin Packing: A Survey, Dorit S. Hochbaum, ed. PWS Publishing Company, 1997.
[5] T.H. Cormen, C.E. Leiserson, and R.L. Rivest, Introduction to Algorithms. The MIT Press, 1989.
[6] M. Farach, “Optimal Suffix Tree Construction with Large Alphabets,” Proc. 38th Ann. Symp. Foundation of Computer Science, pp. 137143, 1997.
[7] M. Farach, P. Ferragina, and S. Muthukrishnan, “Overcoming the Memory Bottleneck in Suffix Tree Construction,” Proc. 39th Symp. Foundations of Computer Science, pp. 174185, 1998.
[8] M. Farach and S. Muthukrishnan, “Optimal Logarithmic Time Randomized Suffix Tree Construction,” Proc. 23rd Int'l Colloquium Automata Languages and Programming, pp. 550561, 1996.
[9] M. FarachColton, P. Ferragina, and S. Muthukrishnan, “On the SortingComplexity of Suffix Tree Construction,” J. ACM, vol. 47, no. 6, pp. 9871011, 2000.
[10] R. Giegerich and S. Kurtz, “From Ukkonen to McCreight and Weiner: A Unifying View of LinearTime Suffix Tree Construction,” Algorithmica, vol. 19, no. 3, pp. 331353, 1997.
[11] R. Giegerich, S. Kurtz, and J. Stoye, “Efficient Implementation of Lazy Suffix Trees,” Proc. Third Int'l Workshop Algorithm Eng., pp. 3042, 1999.
[12] D. Gusfield, Algorithms on Strings, Trees, and Sequences Computer Science and Computational Biology. Cambridge Univ. Press, 1997.
[13] D. Gusfield and J. Stoye, “Linear Time Algorithms for Finding and Representing All Tandem Repeats in a String,” technical report, Computer Science Dept., Univ. of California, Davis, 1998.
[14] D. Harel and R.E. Tarjan, “Fast Algorithms for Finding Nearest Common Ancestors,” SIAM J. Computing, vol. 13, pp. 338–355, May 1984.
[15] E. Hunt, M.P. Atkinson, and R.W. Irving, “A Database Index to Large Biological Sequences,” Proc. 27th Int'l Conf. Very Large Data Bases, pp. 139148, 2001.
[16] E. Hunt, R.W. Irving, and M. Atkinson, “Persistent Suffix Trees and Suffix Binary Search Trees as DNA Sequence,” technical report, Dept. of Computing Science, Univ. of Glasgow, 2000.
[17] J. Kärkkäinen, “Suffix Cactus: A Cross between Suffix Tree and Suffix Array,” Proc. Sixth Symp. Combinatorial Pattern Matching, pp. 191204, 1995.
[18] J. Karkkainen and E. Ukkonen, “Sparse Suffix Trees,” Proc. Second Ann. Int'l Conf. Computing and Combinatorics, pp. 219230, 1996.
[19] S. Kurtz, “Reducing the Space Requirement of Suffix Trees,” Software Practice and Experience, vol. 29, no. 13, pp. 11491171, 1999.
[20] E.M. McCreight, “A SpaceEconomical Suffix Tree Construction Algorithm,” J. ACM, vol. 23, no. 2, pp. 262272, 1976.
[21] G. Navarro, “A Guided Tour to Approximate String Matching,” ACM Computing Surveys, vol. 33, no. 1, pp. 3188, 2001.
[22] G. Navarro and R. BaezaYates, “A New Indexing Method for Approximate String Matching,” Proc. 10th Ann. Symp. Combinatorial Pattern Matching, pp. 163185, 1999.
[23] B. Schieber and U. Vishkin, “On Finding Lowest Common Ancestors: Simplification and Parallelization,” SIAM J. Computing, vol. 17, pp. 12531262, Dec. 1988.
[24] W. Szpankowski, “Asymptotic Properties of Data Compression and Suffix Trees,” IEEE Trans. Information Theory, vol. 39, no. 5, pp. 16471659, 1993.
[25] P. Weiner, “Linear Pattern Matching Algorithm,” Proc. 14th IEEE Symp. Switching and Automata Theory, 1973.
[26] A.D. Wyner and J. Ziv, “Some Asymptotic Properties of the Entropy of a Stationary Ergodic Data Source with Applications to Data Compression,” IEEE Trans. Information Theory, vol. 35, no. 6, 1989.