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External memory BWT and LCP computation for sequence collections with applications

  • Published:2019-03-08 Issue:1 Volume:14 Page:
  • ISSN:1748-7188
  • Container-title:Algorithms for Molecular Biology
  • language:en
  • Short-container-title:Algorithms Mol Biol

Author:

Egidi Lavinia,Louza Felipe A.ORCID,Manzini Giovanni,Telles Guilherme P.

Funder

Fundação de Amparo à Pesquisa do Estado de São Paulo

Ministero dell’Istruzione, dell’Università e della Ricerca

Publisher

Springer Science and Business Media LLC

Subject

Applied Mathematics,Computational Theory and Mathematics,Molecular Biology,Structural Biology

Reference47 articles.

1. Burrows M, Wheeler DJ. A block-sorting lossless data compression algorithm. Technical report, Digital SRC Research Report; 1994.

2. Mäkinen V, Belazzougui D, Cunial F, Tomescu AI. Genome-Scale Algorithm Design: biological sequence analysis in the era of high-throughput sequencing. Cambridge: Cambridge University Press; 2015.

3. Manber U, Myers G. Suffix arrays: a new method for on-line string searches. SIAM J Comput. 1993;22(5):935–48.

4. Gog S, Ohlebusch E. Compressed suffix trees: efficient computation and storage of LCP-values. ACM J Exp Algorith. 2013;18:2.

5. Navarro G, Mäkinen V. Compressed full-text indexes. ACM Comput Surv. 2007;39:1.

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