Efficient maximal repeat finding using the burrows-wheeler transform and wavelet tree

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 2, 2012, Pages 421-429

  Kulekci, M Oguzhan ^a   Vitter, Jeffrey Scott ^b   Xu, Bojian ^c  

^a National Research Institute of Electronics and Cryptology   (Turkey)

^b University of Kansas   (United States)

^c EASTERN WASHINGTON UNIVERSITY   (United States)

Author keywords

Burrows Wheeler transform; maximal repeats; Repeats; wavelet trees

Indexed keywords

AUXILIARY DATA STRUCTURES; BIOLOGICAL FUNCTIONS; BURROWS WHEELER TRANSFORM; DATA COMPRESSOR; DATA SETS; DESKTOP COMPUTER; EXTERNAL MEMORY; GENOMIC SEQUENCE; HUMAN GENOMES; INTERNAL MEMORY; MASSIVE DATA; MAXIMAL REPEATS; NATURAL LANGUAGE TEXT; OPEN-SOURCE SOFTWARES; ORDERS OF MAGNITUDE; PROTEIN DATA; REPEATS; REPETITIVE STRUCTURE; SPACE USAGE; SUFFIX ARRAYS; SUFFIX-TREES; TIMING PERFORMANCE; WAVELET TREE;

DATA STRUCTURES; FORESTRY; GENES; WAVELET TRANSFORMS;

TREES (MATHEMATICS);

DATA; FORESTRY; GENES; MATHEMATICS; TREES;

PROTEIN;

ALGORITHM; BIOLOGY; CHEMISTRY; GENETICS; GENOME; NATURAL LANGUAGE PROCESSING; PROCEDURES; PROTEIN DATABASE; SEQUENCE ANALYSIS; ARTICLE; METHODOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENOME; NATURAL LANGUAGE PROCESSING; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 84856440630     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.127     Document Type: Article

References (42)

1. V. Becher, A. Deymonnaz, and P.A. Heiber, "Efficient Computation of All Perfect Repeats in Genomic Sequences of Up To Half a Gigabyte, with a Case Study on the Human Genome," Bioinformatics, vol. 25, no. 14, pp. 1746-1753, 2009.
2. B. Behzadi and F.L. Fessant, "DNA Compression Challenge Revisited: A Dynamic Programming Approach," Proc. Ann. Symp. Combinatorial Pattern Matching, 2005.
3. G. Benson, "Tandem Repeats Finder: A Program to Analyze DNA Sequences," Nucleic Acids Research, vol. 27, no. 2, pp. 573-580, 1999. (Pubitemid 29210025)
4. M. Burrows and D.J. Wheeler, "A Block Sorting Data Compression Algorithm," technical report, Digital Systems Research Center, 1994.
5. A.T. Castelo, W. Martins, and G.R. Gao, "Troll-Tandem Repeat Occurrence Locator," Bioinformatics, vol. 18, no. 4, pp. 634-636, 2002.
6. R. Dementiev, J. Kärkkäinen, J. Mehnert, and P. Sanders, "Better External Memory Suffix Array Construction," J. Experimental Algorithmics, vol. 12, pp. 1-24, 2008.
7. P. Ferragina and G. Manzini, "Indexing Compressed Text," J. ACM, vol. 52, no. 4, pp. 552-581, 2005. (Pubitemid 43078371)
8. P. Ferragina, G. Manzini, V. Mäkinen, and G. Navarro, "An Alphabet-Friendly FM-Index," Proc. Int'l Symp. String Processing and Information Retrieval (SPIRE), pp. 150-160, 2004.
9. J. Fischer, V. Mäkinen, and N. Välimäki, "Space Efficient String Mining under Frequency Constraints," Proc. IEEE Int'l Conf. Data Mining, pp. 193-202, 2008.
10. R. Grossi, A. Gupta, and J.S. Vitter, "High-Order Entropy-Compressed Text Indexes," Proc. ACM-SIAM Symp. Discrete Algorithms, pp. 841-850, 2003.
11. R. Grossi and J.S. Vitter, "Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching," SIAM J. Computing, vol. 35, no. 32, pp. 378-407, 2005.
12. D. Gusfield, Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge Univ. Press, 1997.
13. W.-K. Hon, T.-W. Lam, K. Sadakane, W.-K. Sung, and S.-M. Yiu, "A Space and Time Efficient Algorithm for Constructing Compressed Suffix Arrays," Algorithmica, vol. 48, no. 1, pp. 23-36, 2007. (Pubitemid 47136627)
14. W.-K. Hon, K. Sadakane, and W.-K. Sung, "Breaking a Time-And-Space Barrier in Constructing Full-Text Indices," SIAM J. Computing, vol. 38, no. 6, pp. 2162-2178, 2009.
15. J. Kärkkäinen, "Fast BWT in Small Space by Blockwise Suffix Sorting," Theoretical Computer Science, vol. 387, no. 3, pp. 249-257, 2007. (Pubitemid 47633442)
16. J. Kärkkäinen, G. Manzini, and S.J. Puglisi, "Permuted Longest-Common-Prefix Array," Proc. 20th Ann. Symp. Combinatorial Pattern Matching (CPM), pp. 181-192, 2009.
17. T. Kasai, G. Lee, H. Arimura, S. Arikawa, and K. Park, "Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications," Proc. Ann. Symp. Combinatorial Pattern Matching, pp. 181-192, 2001. (Pubitemid 33298873)
18. M.O. Kü lekci, J.S. Vitter, and B. Xu, "Time-And Space-Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Trees," Proc. IEEE Int'l Conf. Bioinformatics and Biomedicine (BIBM), pp. 622-625, 2010.
19. S. Kurtz, "Reducing the Space Requirements of Suffix Trees," Software-Practice and Experience, vol. 29, no. 13, pp. 1149-1171, 1999. (Pubitemid 129303954)
20. S. Kurtz, J.V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, and R. Giegerich, "Reputer: The Manifold Applications of Repeat Analysis on a Genomic Scale," Nucleic Acids Research, vol. 29, no. 22, pp. 4633-4642, 2001. (Pubitemid 33095024)
21. S. Kurtz and C. Schleiermacher, "Reputer: Fast Computation of Maximal Repeats in Complete Genomes," Bioinformatics, vol. 15, no. 5, pp. 426-427, 1999. (Pubitemid 29312632)
22. A. Lefebvre, T. Lecroq, H. Dauchel, and J. Alexandre, "FORRepeats: Detects Repeats on Entire Chromosomes and between Genomes," Bioinformatics, vol. 19, no. 3, pp. 319-326, 2003. (Pubitemid 36284931)
23. R. Lippert, "Space-Efficient Whole Genome Comparisons with Burrows-Wheeler Transforms," J. Computational Biology, vol. 12, no. 4, pp. 407-415, 2005. (Pubitemid 40696479)
24. R.A. Lippert, C.M. Mobarry, and B. Walenz, "A Space-Efficient Construction of the Burrows-Wheeler Transform for Genomic Data," J. Computational Biology, vol. 12, no. 7, pp. 943-951, 2005. (Pubitemid 41384390)
25. X. Liu and L. Wang, "Finding the Region of Pseudo-Periodic Tandem Repeats in Biological Sequences," Algorithms for Molecular Biology, vol. 1, no. 1, p. 2, 2006.
26. V. Mäkinen, "Compact Suffix Array: A Space-Efficient Full-Text Index," Fundamenta Informaticae, vol. 56, pp. 191-210, Oct. 2002.
27. G. Manzini, "Two Space Saving Tricks for Linear Time lcp Array Computation," Proc. Scandinavian Workshop Algorithm Theory, pp. 372-383, 2004.
28. G. Manzini and M. Rastero, "A Simple and Fast DNA Compressor," Software-Practice and Experience, vol. 34, pp. 1397-1411, 2004.
29. H.M. Martinez, "An Efficient Method for Finding Repeats in Molecular Sequences," Nucleic Acids Research, vol. 11, no. 13, pp. 4629-4634, 1983.
30. E.H. McConkey, Human Genetics: The Molecular Revolution. Jones and Bartlett, 1993.
31. J.C. Na and K. Park, "Alphabet-Independent Linear-Time Construction of Compressed Suffix Arrays Using o(nlogn)-Bit Working Space," Theoretical Computer Science, vol. 385, nos. 1-3, pp. 127-136, 2007. (Pubitemid 47419161)
32. G. Navarro and V. Mäkinen, "Compressed Full-Text Indexes," ACM Computing Surveys, vol. 39, no. 1, 2007.
33. E. Ohlebusch, S. Gog, and A. Kü gell, "Computing Matching Statistics and Maximal Exact Matches on Compressed Full-Text Indexes," Proc. 17th Int'l Conf. String Processing and Information Retrieval (SPIRE), pp. 347-358, 2010.
34. D. Okanohara and K. Sadakane, "A Linear-Time Burrows-Wheeler Transform Using Induced Sorting," Proc. Int'l Symp. String Processing and Information Retrieval, pp. 90-101, 2009.
35. A. Poddar, N. Chandra, M. Ganapathiraju, K. Sekar, J. Klein-Seetharaman, R. Judith, R. Reddy, and N. Balakrishnan, "Evolutionary Insights from Suffix Array-based Genome Sequence Analysis," J. Biosciences, vol. 32, no. 5, pp. 871-881, 2007. (Pubitemid 47435519)
36. R. Raman, V. Raman, and S.S. Rao, "Succinct Indexable Dictionaries with Applications to Encoding k-Ary Trees, Prefix Sums and Multisets," ACM Trans. Algorithms, vol. 3, no. 4, p. 43, 2007.
37. K. Sadakane, "Succinct Representations of lcp Information and Improvements in the Compressed Suffix Arrays," Proc. Ann. ACM-SIAM Symp. Discrete Algorithms, pp. 225-232, 2002.
38. S. Saha, S. Bridges, Z.V. Magbanua, and D.G. Peterson, "Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences," Tropical Plant Biology, vol. 1, no. 1, pp. 85-96, 2008.
39. S. Saha, S. Bridges, Z.V. Magbanua, and D.G. Peterson, "Empirical Comparison of ab Initio Repeat Finding Programs," Nucleic Acids Research, vol. 36, no. 7, pp. 2284-2294, 2008. (Pubitemid 351567001)
40. J. Sirén, "Sampled Longest Common Prefix Array," Proc. Ann. Symp. Combinatorial Pattern Matching (CPM), pp. 227-237, 2010.
41. N. Välimäki, V. Mäkinen, W. Gerlach, and K. Dixit, "Engineering a Compressed Suffix Tree Implementation," J. Experimental Algorithmics, vol. 14, pp. 2:4.2-2:4.23, 2010.
42. J.S. Vitter, Algorithms and Data Structures for External Memory, Foundations and Trends in Theoretical Computer Science. Now Publishers, 2008.