Abstract
To compute Burrows-Wheeler Transform (BWT), one usually builds a suffix array (SA) first, and then obtains BWT using SA, which requires much redundant working space. In previous studies to compute BWT directly [5,12], one constructs BWT incrementally, which requires O(n logn) time where n is the length of the input text. We present an algorithm for computing BWT directly in linear time by modifying the suffix array construction algorithm based on induced sorting [15]. We show that the working space is O(n logσloglog σ n) for any σ where σ is the alphabet size, which is the smallest among the known linear time algorithms.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Burrows, M., Wheeler, D.J.: A block-sorting lossless data compression algorithm. Technical report, Digital Equipment Corporation (1994)
Farach, M.: Optimal Suffix Tree Construction with Large Alphabets. In: Proc. of FOCS, pp. 137–143 (1997)
Ferragina, P., Giancarlo, R., Manzini, G., Sciortino, M.: Compression boosting in optimal linear time. Journal of the ACM 52(4), 688–713 (2005)
Grossi, R., Vitter, J.S.: Compressed suffix arryas and suffix trees with applications to text indexing and string matching. Computing 35(2), 378–407 (2005)
Hon, W.-K., Lam, T.-W., Sadakane, K., Sung, W.-K., Yiu, S.-M.: A space and time efficient algorithm for constructing compressed suffix arrays. Algorithmica 48(1), 23–36 (2007)
Hon, W.K., Sadakane, K., Sung, W.K.: Breaking a Time-and-Space Barrier in Constructing Full-Text Indices. SIAM Journal on Computing 38(6), 2162–2178 (2009)
Kärkkäinen, J.: Fast bwt in small space by blockwise suffix sorting. Theoretical Computer Science 387(3), 249–257 (2007)
Kärkkäinen, J., Sanders, P., Burkhardt, S.: Linear work suffix array construction. ACM 53(6), 918–936 (2006)
Kim, D.-K., Sim, J.S., Park, H.-J., Park, K.: Linear-time construction of suffix arrays. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 186–199. Springer, Heidelberg (2003)
Ko, P., Aluru, S.W.: Space-efficient linear time construction of suffix arrays. Discrete Algorithm 3, 143–156 (2005)
Lippert, R.: Space-efficient whole genome comparisons with burrows-wheeler transforms. j. of computational biology. Computational Biology 12(4) (2005)
Lippert, R., Mobarry, C., Walenz, B.: A space-efficient construction of the burrows wheeler transform for genomic data. In: Computational Biology (2005)
Chae Na, J., Park, K.: Alphabet-independent linear-time construction of compressed suffix arrays using o(nlogn)-bit working space. Theoretical Computer Science 385(1-3), 127–136 (2007)
Navarro, G., Mäkinen, V.: Compressed full-text indexes. ACM Computing Surveys 39(1), 2–61 (2007)
Nong, G., Zhang, S., Chan, W.H.: Linear suffix array construction by almost pure induced-sorting. In: Proc. of DCC (2009)
Raman, R., Raman, V., Rao, S.S.: Succinct indexable dictionaries with applications to encoding k-ary trees and multisets. In: Proc. of SODA, pp. 233–242 (2002)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Okanohara, D., Sadakane, K. (2009). A Linear-Time Burrows-Wheeler Transform Using Induced Sorting. In: Karlgren, J., Tarhio, J., Hyyrö, H. (eds) String Processing and Information Retrieval. SPIRE 2009. Lecture Notes in Computer Science, vol 5721. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03784-9_9
Download citation
DOI: https://doi.org/10.1007/978-3-642-03784-9_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-03783-2
Online ISBN: 978-3-642-03784-9
eBook Packages: Computer ScienceComputer Science (R0)