Higher classification accuracy of short metagenomic reads by discriminative spaced k-mers

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 9289, Issue , 2015, Pages 286-295

  Ounit, Rachid ^a   Lonardi, Stefano ^a  

^a University of California ^*  (United States)

Author keywords

Classification; Discriminative spaced k mers; Metagenomics; Microbiome; Short metagenomic reads

Indexed keywords

BIOINFORMATICS; CLASSIFICATION (OF INFORMATION); COMPETITION;

CLASSIFICATION ACCURACY; COMPETITIVE ADVANTAGE; COMPUTATIONAL DEMANDS; DISCRIMINATIVE SPACED K-MERS; ENVIRONMENTAL SCIENCE; METAGENOMICS; MICROBIOME; SHORT METAGENOMIC READS;

ALGORITHMS;

EID: 84947788619     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-662-48221-6_21     Document Type: Conference Paper

References (26)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. J. Mol. Biol. 215(3), 403–410 (1990)
2. Bao, E., Jiang, T., Kaloshian, I., Girke, T.: Seed: efficient clustering of nextgeneration sequences. Bioinformatics 27(18), 2502–2509 (2011)
3. Bazinet, A.L., Cummings, M.P.: A comparative evaluation of sequence classification programs. BMC Bioinformatics 13(1), 92 (2012)
4. Brady, A., Salzberg, S.: PhymmBL expanded: confidence scores, custom databases, parallelization and more. Nat. Methods 8(5), 367–367 (2011)
5. Brown, D.G., Li, M., Ma, B.: A tutorial of recent developments in the seeding of local alignment. J. Bioinform. Comput. Biol. 2(04), 819–842 (2004)
6. Choi, K.P., Zeng, F., Zhang, L.: Good spaced seeds for homology search. In: Proceedings of Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004, pp. 379–386. IEEE (2004)
7. Human Microbiome Project Consortium: A framework for human microbiome research. Nature 486(7402), 215–221 (2012)
8. Felczykowska, A., Bloch, S.K., Nejman-Falenczyk, B., Baranska, S.: Metagenomic approach in the investigation of new bioactive compounds in the marine environment. Acta Biochim. Pol. 59, 501–505 (2012)
9. Huson, D.H., Auch, A.F., Qi, J., Schuster, S.C.: MEGAN analysis of metagenomic data. Genome Res. 17(3), 377–386 (2007)
10. Huttenhower, C., Gevers, D., Knight, R., Abubucker, S., Badger, J., Chinwalla, A., et al.: Structure, function and diversity of the healthy human microbiome. Nature 486(7402), 207–214 (2012)
11. Ilie, L., Ilie, S.: Multiple spaced seeds for homology search. Bioinformatics 23(22), 2969–2977 (2007)
12. Ilie, L., Ilie, S., Bigvand, A.M.: Speed: fast computation of sensitive spaced seeds. Bioinformatics 27(17), 2433–2434 (2011)
13. Li, M., Ma, B., Kisman, D., Tromp, J.: Patternhunter ii: highly sensitive and fast homology search. J. Bioinform. Comput. Biol. 2(03), 417–439 (2004)
14. Li, M., Ma, B., Zhang, L.: Superiority and complexity of the spaced seeds. In: Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithm. Society for Industrial and Applied Mathematics, pp. 444–453 (2006)
15. Lindgreen, S., Adair, K.L., Gardner, P.: An Evaluation of the Accuracy and Speed of Metagenome Analysis Tools. Cold Spring Harbor Laboratory Press (2015). doi:10.1101/017830
16. Liu, B., Gibbons, T., Ghodsi, M., Treangen, T., Pop, M.: Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics 12(Suppl 2), S4 (2011)
17. Ma, B., Tromp, J., Li, M.: Patternhunter: faster and more sensitive homology search. Bioinformatics 18(3), 440–445 (2002)
18. Mueller, R.S., Bryson, S., Kieft, B., Li, Z., Pett-Ridge, J., Chavez, F., Hettich, R.L., Pan, C., Mayali, X.: Metagenome sequencing of a coastal marine microbial community from Monterey Bay, California. Genome Announc. 3(2), e00341-15 (2015)
19. Ounit, R., Wanamaker, S., Close, T.J., Lonardi, S.: Clark: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics 16(1), 236 (2015)
20. Pace, N.R.: Mapping the tree of life: progress and prospects. Microbiol. Mol. Biol. Rev. 73(4), 565–576 (2009)
21. Rosen, G.L., Reichenberger, E.R., Rosenfeld, A.M.: NBC: the naive bayes classification tool webserver for taxonomic classification of metagenomic reads. Bioinformatics 27(1), 127–129 (2011)
22. Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., Huttenhower, C.: Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9(8), 811–814 (2012)
23. Sunagawa, S., Mende, D.R., Zeller, G., Izquierdo-Carrasco, F., Berger, S.A., Kultima, J.R., Coelho, L.P., Arumugam, M., Tap, J., Nielsen, H.B., et al.: Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods 10(12), 1196–1199 (2013)
24. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W., et al.: Environmental genome shotgun sequencing of the Sargasso Sea. Science 304(5667), 66–74 (2004)
25. Wood, D., Salzberg, S.: Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15(3), R46 (2014)
26. Zhang, Z., Schwartz, S., Wagner, L., Miller, W.: A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7(1–2), 203–214 (2000)