S. Altschul, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-413, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

N. Askitis and J. Zobel, Redesigning the string hash table, burst trie, and BST to exploit cache, Journal of Experimental Algorithmics, vol.15, p.15, 2010.
DOI : 10.1145/1671970.1921704

L. Bomar, M. Maltz, S. Colston, and J. Graf, Directed Culturing of Microorganisms Using Metatranscriptomics, mBio, vol.2, issue.2, 2011.
DOI : 10.1128/mBio.00012-11

J. Cannone, The comparative rna web (crw) site: An online database of comparative sequence and structure information for ribosomal, intron, and other rnas, BMC Bioinformatics, vol.3, issue.1, p.15, 2002.
DOI : 10.1186/1471-2105-3-15

S. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-763, 1998.
DOI : 10.1093/bioinformatics/14.9.755

R. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, issue.19, pp.2460-2461, 2010.
DOI : 10.1093/bioinformatics/btq461

J. Gilbert and M. Hughes, Gene Expression Profiling: Metatranscriptomics, Mol. Biol, vol.733, pp.195-205, 2011.
DOI : 10.1007/978-1-61779-089-8_14

S. Heinz, J. Zobel, W. , and H. , Burst tries: a fast, efficient data structure for string keys, ACM Transactions on Information Systems, vol.20, issue.2, pp.192-223, 2002.
DOI : 10.1145/506309.506312

Y. Huang, P. Gilna, L. , and W. , Identification of ribosomal RNA genes in metagenomic fragments, Bioinformatics, vol.25, issue.10, pp.1338-1340, 2009.
DOI : 10.1093/bioinformatics/btp161

J. Lee, H. Yi, C. , and J. , rRNASelector: A computer program for selecting ribosomal RNA encoding sequences from metagenomic and metatranscriptomic shotgun libraries, The Journal of Microbiology, vol.21, issue.4, pp.689-91, 2011.
DOI : 10.1007/s12275-011-1213-z

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-60, 2009.
DOI : 10.1093/bioinformatics/btp324

W. Ludwig, ARB: a software environment for sequence data, Nucleic Acids Research, vol.32, issue.4, pp.1363-1371, 2004.
DOI : 10.1093/nar/gkh293

J. Mears, Modeling a Minimal Ribosome Based on Comparative Sequence Analysis, Journal of Molecular Biology, vol.321, issue.2, pp.215-249, 2002.
DOI : 10.1016/S0022-2836(02)00568-5

S. Mihov and K. Schulz, Fast Approximate Search in Large Dictionaries, Computational Linguistics, vol.22, issue.1, pp.451-477, 2004.
DOI : 10.1002/spe.4380250307

P. Mitankin, Universal Levenshtein Automata. Building and Properties, 2005.

E. Nawrocki, D. Kolbe, and S. Eddy, Infernal 1.0: inference of RNA alignments, Bioinformatics, vol.25, issue.10, pp.1335-1342, 2009.
DOI : 10.1093/bioinformatics/btp157

V. Nygaard, Limitations of mrna amplification from small-size cell samples, BMC Genomics, vol.6, issue.147, 2005.

E. Pruesse, SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Research, vol.35, issue.21, pp.7188-7196, 2007.
DOI : 10.1093/nar/gkm864

D. Richter, F. Ott, A. Auch, R. Schmid, and D. Huson, A sequencing simulator for genomics and metagenomics, PLoS ONE, vol.3, 2008.

R. Schmieder, Y. Lim, and R. Edwards, Identification and removal of ribosomal RNA sequences from metatranscriptomes, Bioinformatics, vol.28, issue.3, pp.433-435, 2012.
DOI : 10.1093/bioinformatics/btr669

K. Schulz and S. Mihov, Fast string correction with Levenshtein automata, International Journal on Document Analysis and Recognition, vol.5, issue.1, pp.67-85, 2002.
DOI : 10.1007/s10032-002-0082-8

Y. Shi, G. Tyson, and E. Delong, Metatranscriptomics reveals unique microbial small RNAs in the ocean???s water column, Nature, vol.20, issue.7244, p.459, 2009.
DOI : 10.1038/nature08055

R. Sinha and J. Zobel, Cache-conscious sorting of large sets of strings with dynamic tries, Journal of Experimental Algorithmics, vol.9, issue.es, 2004.
DOI : 10.1145/1005813.1041517

R. Sinha, J. Zobel, and D. Ring, Cache-efficient string sorting using copying, Journal of Experimental Algorithmics, vol.11, p.11, 2006.
DOI : 10.1145/1187436.1187439

F. Stewart, Metatranscriptomics analysis of sulfur oxidation genes in the endosymbiont of solemnya velum, Front. Microbiol, vol.2, issue.134, 2011.