DySC: Software for greedy clustering of 16S rRNA reads

Bioinformatics

Volumn 28, Issue 16, 2012, Pages 2182-2183

  Zheng, Zejun ^a   Kramer, Stefan ^a   Schmidt, Bertil ^a  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARTICLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; GENETICS; METAGENOME; METHODOLOGY; SEQUENCE ANALYSIS;

CLUSTER ANALYSIS; METAGENOME; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84865105014     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts355     Document Type: Article

References (13)

1. Cai, Y. and Sun, Y. (2011) ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time. Nucleic Acid Res., 39, e95.
2. Cole, J.R. et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acid Res., 37, D141-D145.
3. Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
4. Edgar, R.C. et al. (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27, 2194-2200.
5. Holm, L. and Sander, C. (1998) Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics, 14, 423-429.
6. Huse, S.M. et al. (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol., 12, 1889-1898.
7. Li, W. and Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
8. Li, W. et al. (2001) Clustering of highly homologous sequences to reduce the size of large protein database. Bioinformatics, 17, 282-283.
9. Nawrocki, E.P. et al. (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
10. Schloss, P.D. (2009) A high-throughput DNA sequence aligner for microbial ecology studies. PLoS One, 4, e8230.
11. Sun, Y. et al. (2009) ESPRIT: estimating species richness using large collections of 16S rDNA pyrosequences. Nucleic Acids Res., 37, e76.
12. Sun, Y. et al. (2011)Alarge-scale benchmark study of existing algorithms for taxonomyindependent microbial community analysis. Brief Bioinform., 13, 107-121.
13. Turnbaugh, P.J. et al. (2009) A core gut microbiome in obese and lean twins. Nature, 457, 480-484.