Journaled string tree-a scalable data structure for analyzing thousands of similar genomes on your laptop

Bioinformatics

Volumn 30, Issue 24, 2014, Pages 3499-3505

  Rahn, René ^a   Weese, David ^a   Reinert, Knut ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; COMPUTER; DNA SEQUENCE; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

ALGORITHMS; COMPUTERS; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA;

EID: 84922712385     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu438     Document Type: Article

References (32)

1. Altshuler, D. et al. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
2. Auton, A. et al. (2012) A fine-scale chimpanzee genetic map from population sequencing. Science, 336, 193-198.
3. Baeza-Yates, R. and Gonnet, G. H. (1992) A new approach to text searching. Commun. ACM, 35, 74-82.
4. Ball, M. P. et al. (2012) A public resource facilitating clinical use of genomes. Proc. Natl Acad. Sci. USA, 109, 11920-11927.
5. Barton, C. et al. (2013) Querying highly similar sequences. Int. J. Comput. Biol. Drug Des., 6, 119-130.
6. De Bona, F. et al. (2008) Optimal spliced alignments of short sequence reads. Bioinformatics, 24, i174-i180.
7. Deorowicz, S. et al. (2013) Genome compression: a novel approach for large collections. Bioinformatics, 29, 2572-2578.
8. Deorowicz, S. and Grabowski, S. (2011) Robust relative compression of genomes with random access. Bioinformatics, 27, 2979-2986.
9. Döring, A. et al. (2008) SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9, 11.
10. Durbin, R. M. et al. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
11. Ferragina, P. and Manzini, G (2000) Opportunistic data structures with applications. In: Proceedings of the 41st Annual Symposium on Foundations of Computer Science. FOCS'00, pp. 390-398.
12. Frazer, K. et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-861.
13. Henikoff, J. G. et al. (2000) Increased coverage of protein families with the blocks database servers. Nucleic Acids Res., 28, 228-230.
14. Horspool, R. N. (1980) Practical fast searching in strings. Softw. Pract. Exper., 10, 501-506.
15. Huang, L. et al. (2013) Short read alignment with populations of genomes. Bioinformatics, 29, i361-i370.
16. Kahn, S. D. (2011) On the future of genomic data. Science, 331, 728-729.
17. Keane, T. M. et al. (2011) Mouse genomic variation and its effect on phenotypes and gene regulation. Nature, 477, 289-294.
18. Kuruppu, S. et al. (2011) Optimized relative lempel-ziv compression of genomes. In: Proceedings of the Thirty-Fourth Australasian Computer Science Conference. Vol. 113, ACSC'11, pp. 91-98.
19. Lam, T. et al. (2010) Indexing similar dna sequences. In: Chen, B. (ed.) Algorithmic Aspects in Information and Management. Vol. 6124 of Lecture Notes in Computer Science. Springer, Berlin Heidelberg, pp. 180-190.
20. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with burrowswheeler transform. Bioinformatics, 25, 1754-1760.
21. Lippert, R. (2005) Space-efficient whole genome comparisons with burrows-wheeler. J. Comput. Biol., 12, 407-415.
22. Loh, P.-R. et al. (2012) Compressive genomics. Nat. Biotechnol., 30, 627-630.
23. Mäkinen, V. et al. (2009) Storage and retrieval of individual genomes. In: Batzoglou, S. (ed.) Research in Computational Molecular Biology. Vol. 5541 of LNCS. Springer, Berlin Heidelberg, pp. 121-137.
24. Myers, E. W. (1999) A fast bit-vector algorithm for approximate string matching based on dynamic programming. J. ACM, 46, 395-415.
25. Pinho, AJ. et al. (2012) GReEn: a tool for efficient compression of genome resequencing data. Nucleic Acids Res., 40, e27.
26. Schneeberger, K. et al. (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biol., 10, R98.
27. Scordis, P. et al. (1999) Fingerprintscan: intelligent searching of the prints motif database. Bioinformatics, 15, 799-806.
28. Sirén, J. et al. (2011) Indexing finite language representation of population genotypes. Algorithms Bioinformatics, 6833, 270-281.
29. The 1000 Genomes Project Consortium. (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65.
30. The International Cancer Genome Consortium. (2010) International network of cancer genome projects. Nature, 464, 993-998.
31. Wandelt, S. and Leser, U. (2012) Adaptive efficient compression of genomes. Algorithms Mol. Biol., 7, 30.
32. Weese, D. et al. (2012) Razers 3: faster, fully sensitive read mapping. Bioinformatics, 28, 2592-2599.