This is a preview of subscription content, log in via an institution to check access.
References
Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402.
Huang Y, Niu B, Gao Y, et al. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics. 2010;26:680–2.
Huse SM, Welch DM, Morrison HG, et al. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol. 2010;12:1889–98.
Kunin V, Engelbrektson A, Ochman H, et al. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol. 2010;12:118–23.
Li W. Analysis and comparison of very large metagenomes with fast clustering and functional annotation. BMC Bioinforma. 2009;10:359.
Li WZ, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9.
Li W, Wooley JC, Godzik A. Probing metagenomics by rapid cluster analysis of very large datasets. PLoS ONE. 2008;3:e3375.
Li W, Fu L, Niu B, Wu S, Wooley J. Ultrafast clustering algorithms for metagenomic sequence analysis. Brief Bioinform. 2012. doi:10.1093/bib/bbs035.
Niu B, Fu L, Sun S, et al. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinforma. 2010;11:187.
Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65.
Quince C, Lanzén A, Curtis TP, et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods. 2009;6:639.
Quince C, Lanzen A, Davenport RJ, et al. Removing noise from pyrosequenced amplicons. BMC Bioinforma. 2011;12:38.
Reeder J, Knight R. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods. 2010;7:668–9.
Schloss PD, Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005;71:1501–6.
Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.
Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 2011;6(12):e27310.
Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457:480–U487.
White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol. 2009;5:e1000352.
Wu S, Zhu Z, Fu L, et al. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics. 2011;12:444.
Yooseph S, Sutton G, Rusch DB, et al. The sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLoS Biol. 2007;5:e16.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media New York
About this entry
Cite this entry
Niu, B., Wu, S., Li, W. (2013). Clustering-Based HMP Sequence Comparison. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_90-8
Download citation
DOI: https://doi.org/10.1007/978-1-4614-6418-1_90-8
Received:
Accepted:
Published:
Publisher Name: Springer, New York, NY
Online ISBN: 978-1-4614-6418-1
eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences