Efficient counting of k-mers in DNA sequences using a bloom filter

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Melsted, Páll ^a   Pritchard, Jonathan K ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL SPEED; DNA SEQUENCE DATA; MEMORY REQUIREMENTS; PROBABILISTIC DATA; REDUCED MEMORY REQUIREMENTS; REFERENCE IMPLEMENTATION; SEQUENCING ERRORS; TRANSCRIPTOME ASSEMBLIES;

ALGORITHMS; BIOINFORMATICS; DATA STRUCTURES; ERROR CORRECTION;

DNA SEQUENCES;

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER; COMPUTER PROGRAM; DNA SEQUENCE; HAPLOTYPE MAP; HUMAN; INSTRUMENTATION; METHODOLOGY; PROBABILITY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTERS; HAPMAP PROJECT; HUMANS; PROBABILITY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 81155158421     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-333     Document Type: Article

References (23)

1. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. PLoS ONE 2008, 3(10):e3376. 10.1371/journal.pone.0003376, 2557064, 18852878., http://dx.doi.org/10.1371/journal.pone.0003376
2. Andolfatto P, Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Research 2011, http://genome.cshlp.org/content/early/2011/02/28/gr.115402.110.abstract
3. Pevzner PA, Tang H, Waterman MS. An Eulerian path approach to DNA fragment assembly. Proceedings of the National Academy of Sciences of the United States of America 2001, 98(17):9748-9753. 10.1073/pnas.171285098, 55524, 11504945., http://www.pnas.org/content/98/17/9748.abstract
4. Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 2008, 18(5):821-829. 10.1101/gr.074492.107, 2336801, 18349386., http://genome.cshlp.org/content/18/5/821.abstract
5. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Research 2008, 18(5):810-820. 10.1101/gr.7337908, 2336810, 18340039., http://genome.cshlp.org/content/18/5/810.abstract
6. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: A parallel assembler for short read sequence data. Genome Research 2009, 19(6):1117-1123. 10.1101/gr.089532.108, 2694472, 19251739., http://genome.cshlp.org/content/19/6/1117.abstract
7. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J. De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 2010, 20(2):265-272. 10.1101/gr.097261.109, 2813482, 20019144., http://genome.cshlp.org/content/20/2/265.abstract
8. Marçais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 2011, 27(6):764-770. 10.1093/bioinformatics/btr011, 21217122., http://bioinformatics.oxfordjournals.org/content/27/6/764.abstract
9. Knuth DE. The art of computer programming, sorting and searching 1998, 3. Redwood City, CA, USA: Addison Wesley Longman Publishing Co., Inc, 2.
10. Conway TC, Bromage AJ. Succinct data structures for assembling large genomes. Bioinformatics 2011, 27(4):479-486. 10.1093/bioinformatics/btq697, 21245053., http://bioinformatics.oxfordjournals.org/content/27/4/479.abstract
11. Li R, Fan W, Tian G, et al. The sequence and de novo assembly of the giant panda genome. Nature 2010, 463(7279):311-317. 10.1038/nature08696, 20010809., http://dx.doi.org/10.1038/nature08696
12. Kelley D, Schatz M, Salzberg S. Quake: quality-aware detection and correction of sequencing errors. Genome Biology 2010, 11(11):R116., http://genomebiology.com/2010/11/11/R116
13. Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proceedings of the National Academy of Sciences 2011, 108(4):1513-1518., http://www.pnas.org/content/108/4/1513.abstract
14. Shi H, Schmidt B, Liu W, Müller-Wittig W. A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware. Journal of Computational Biology 2010, 17(4):603-615. 10.1089/cmb.2009.0062, 20426693., http://www.liebertonline.com/doi/abs/10.1089/cmb.2009.0062
15. Bar-Yossef Z, Jayram T, Kumar R, Sivakumar D, Trevisan L. Counting Distinct Elements in a Data Stream. Randomization and Approximation Techniques in Computer Science, Volume 2483 of Lecture Notes in Computer Science 2002, 952-952. Springer Berlin/Heidelberg, Rolim J, Vadhan S., http://dx.doi.org/10.1007/3-540-45726-7_1
16. Bloom BH. Space/time trade-offs in hash coding with allowable errors. Commun ACM 1970, 13:422-426., http://doi.acm.org/10.1145/362686.362692
17. Stranneheim H, Käller M, Allander T, Andersson B, Arvestad L, Lundeberg J. Classification of DNA sequences using Bloom filters. Bioinformatics 2010, 26(13):1595-1600. 10.1093/bioinformatics/btq230, 2887045, 20472541., http://bioinformatics.oxfordjournals.org/content/26/13/1595.abstract
18. Krishnamurthy P, Buhler J, Chamberlain R, Franklin M, Gyang K, Jacob A, Lancaster J. Biosequence Similarity Search on the Mercury System. The Journal of VLSI Signal Processing 2007, 49:101-121., http://dx.doi.org/10.1007/s11265-007-0087-0
19. Broder A, Mitzenmacher M. Network Applications of Bloom Filters: A Survey. Internet Mathematics 2004, 1(4):485-509.
20. Fan L, Cao P, Almeida J, Broder AZ. Summary cache: a scalable wide-area web cache sharing protocol. IEEE/ACM Trans Netw 2000, 8:281-293., http://dx.doi.org/10.1109/90.851975
21. Pagh A, Pagh R, Rao SS. An optimal Bloom filter replacement. Proceedings of the sixteenth annual ACM-SIAM symposium on Discrete algorithms, SODA '05, Philadelphia, PA, USA: Society for Industrial and Applied Mathematics 2005, 823-829., http://portal.acm.org/citation.cfm?id=1070432.1070548
22. Purcell C, Harris T. Non-blocking Hashtables with Open Addressing. Distributed Computing, Volume 3724 of Lecture Notes in Computer Science 2005, 108-121. Springer Berlin/Heidelberg, Fraigniaud P., http://dx.doi.org/10.1007/11561927_10
23. The 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing. Nature 2010, 467(7319):1061-1073. 10.1038/nature09534, 3042601, 20981092, The 1000 Genomes Project Consortium.