Abstract
Relative Lempel-Ziv (RLZ) is a popular algorithm for compressing databases of genomes from individuals of the same species when fast random access is desired. With Kuruppu et al.’s (SPIRE 2010) original implementation, a reference genome is selected and then the other genomes are greedily parsed into phrases exactly matching substrings of the reference. Deorowicz and Grabowski (Bioinformatics, 2011) pointed out that letting each phrase end with a mismatch character usually gives better compression because many of the differences between individuals’ genomes are single-nucleotide substitutions. Ferrada et al. (SPIRE 2014) then pointed out that also using relative pointers and run-length compressing them usually gives even better compression. In this paper we generalize Ferrada et al.’s idea to handle well also short insertions, deletions and multi-character substitutions. We show experimentally that our generalization achieves better compression than Ferrada et al.’s implementation with comparable random-access times.
Supported by the Academy of Finland through grants 258308, 268324, 284598 and 285221 and by the Wellcome Trust grant 098051. Parts of this work were done during the second author’s visit to the University of Helsinki and during the third author’s visits to Illumina Cambridge Ltd. and the University of A Coruña, Spain.
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References
Ziv, J., Lempel, A.: A universal algorithm for sequential data compression. IEEE Trans. Inf. Theor. 23, 337–343 (1977)
Kuruppu, S., Puglisi, S.J., Zobel, J.: Relative Lempel-Ziv compression of genomes for large-scale storage and retrieval. In: Chavez, E., Lonardi, S. (eds.) SPIRE 2010. LNCS, vol. 6393, pp. 201–206. Springer, Heidelberg (2010)
Ziv, J., Merhav, N.: A measure of relative entropy between individual sequences with application to universal classification. IEEE Trans. Inf. Theor. 39, 1270–1279 (1993)
Hoobin, C., Puglisi, S.J., Zobel, J.: Sample selection for dictionary-based corpus compression. In: Proceedings of SIGIR, pp. 1137–1138 (2011)
Hoobin, C., Puglisi, S.J., Zobel, J.: Relative Lempel-Ziv factorization for efficient storage and retrieval of web collections. Proc. VLDB 5, 265–273 (2011)
Deorowicz, S., Grabowski, S.: Robust relative compression of genomes with random access. Bioinformatics 27, 2979–2986 (2011)
Ferrada, H., Gagie, T., Gog, S., Puglisi, S.J.: Relative Lempel-Ziv with constant-time random access. In: Moura, E., Crochemore, M. (eds.) SPIRE 2014. LNCS, vol. 8799, pp. 13–17. Springer, Heidelberg (2014)
Kärkkäinen, J., Kempa, D., Puglisi, S.J.: Hybrid compression of bitvectors for the FM-index. In: Proceedings of DCC, pp. 302–311 (2014)
Deorowicz, S., Danek, A., Niemiec, M.: GDC2: compression of large collections of genomes. Sci. Rep. 5, 1–12 (2015)
Ferragina, P., Manzini, G.: Indexing compressed text. J. ACM 52, 552–581 (2005)
Burrows, M., Wheeler, D.J.: A block sorting lossless data compression algorithm. Technical report 124, Digital Equipment Corporation (1994)
Belazzougui, D., Gagie, T., Gog, S., Manzini, G., Sirén, J.: Relative FM-indexes. In: Moura, E., Crochemore, M. (eds.) SPIRE 2014. LNCS, vol. 8799, pp. 52–64. Springer, Heidelberg (2014)
Boucher, C., Bowe, A., Gagie, T., Manzini, G., Sirén, J.: Relative select. In: Iliopoulos, C., Puglisi, S., Yilmaz, E. (eds.) SPIRE 2015. LNCS, vol. 9309, pp. 149–155. Springer, Heidelberg (2015)
Léonard, M., Mouchard, L., Salson, M.: On the number of elements to reorder when updating a suffix array. J. Discrete Algorithms 11, 87–99 (2012)
Gagie, T., Navarro, G., Puglisi, S.J., Sirén, J.: Relative compressed suffix trees. Technical report 1508.02550 (2015). arxiv.org
Okanohara, D., Sadakane, K.: Practical entropy-compressed rank/select dictionary. In: Proceedings of ALENEX (2007)
Raman, R., Raman, V., Satti, S.R.: Succinct indexable dictionaries with applications to encoding k-ary trees, prefix sums and multisets. ACM Trans. Algorithms 3, 43 (2007)
Farruggia, A., Ferragina, P., Venturini, R.: Bicriteria data compression. In: Proceedings of SODA, pp. 1582–1595 (2014)
Farruggia, A., Ferragina, P., Venturini, R.: Bicriteria data compression: efficient and usable. In: Schulz, A.S., Wagner, D. (eds.) ESA 2014. LNCS, vol. 8737, pp. 406–417. Springer, Heidelberg (2014)
Brudno, M., Malde, S., Poliakov, A., Do, C.B., Couronne, O., Dubchak, I., Batzoglou, S.: Glocal alignment: finding rearrangements during alignment. In: Proceedings of ISMB, pp. 54–62 (2003)
Kubincová, P.: Mapping between genomes. Bachelor thesis, Comenius University, Slovakia Supervised by Broňa Brejová (2014)
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Cox, A.J., Farruggia, A., Gagie, T., Puglisi, S.J., Sirén, J. (2016). RLZAP: Relative Lempel-Ziv with Adaptive Pointers. In: Inenaga, S., Sadakane, K., Sakai, T. (eds) String Processing and Information Retrieval. SPIRE 2016. Lecture Notes in Computer Science(), vol 9954. Springer, Cham. https://doi.org/10.1007/978-3-319-46049-9_1
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