-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
0022552744
-
Multiple sequence alignment
-
Bacon, D. J. and Anderson, W. F. 1986. Multiple sequence alignment. J. Mol. Biol. 191, 153-161.
-
(1986)
J. Mol. Biol.
, vol.191
, pp. 153-161
-
-
Bacon, D.J.1
Anderson, W.F.2
-
3
-
-
80051732979
-
ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time
-
doi: 10. 1093/nar/gkr349
-
Cai, Y. and Sun, Y. 2011. ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time. Nucleic Acids Res. doi: 10. 1093/nar/gkr349.
-
(2011)
Nucleic Acids Res
-
-
Cai, Y.1
Sun, Y.2
-
4
-
-
34447248788
-
Clustered sequence representation for fast homology search
-
Cameron, M., Bernstein, Y., and Williams, H. E. 2007. Clustered sequence representation for fast homology search. J. Comput. Biol. 14, 594-614.
-
(2007)
J. Comput. Biol.
, vol.14
, pp. 594-614
-
-
Cameron, M.1
Bernstein, Y.2
Williams, H.E.3
-
5
-
-
0001463548
-
Non-parametric estimation of the number of classes in a population
-
Chao, A. 1984. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 11, 265-270.
-
(1984)
Scand. J. Stat.
, vol.11
, pp. 265-270
-
-
Chao, A.1
-
6
-
-
84945495487
-
Estimating the number of classes via sample coverage
-
Chao, A. L. and Lee, S. M. 1992. Estimating the number of classes via sample coverage. J. Am. Stat. Assoc. 87, 210-217.
-
(1992)
J. Am. Stat. Assoc.
, vol.87
, pp. 210-217
-
-
Chao, A.L.1
Lee, S.M.2
-
7
-
-
77957888370
-
Stopping rules and estimation for recapture debugging with unequal failure rates
-
Chao, A. M., Ma, M. C., and Yang, M. C. K. 1993. Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika80, 193-201.
-
(1993)
Biometrika
, vol.80
, pp. 193-201
-
-
Chao, A.M.1
Ma, M.C.2
Yang, M.C.K.3
-
8
-
-
77950543296
-
The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer
-
Chun, J., Kim, K. Y., Lee, J. H., and Choi, Y. 2010. The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer. BMC Microbiol. 10, 101.
-
(2010)
BMC Microbiol.
, vol.10
, pp. 101
-
-
Chun, J.1
Kim, K.Y.2
Lee, J.H.3
Choi, Y.4
-
9
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
10
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics26, 2460-2461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
11
-
-
67650021209
-
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
-
Hamady, M. and Knight, R. 2009. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res. 19, 1141-1152.
-
(2009)
Genome Res.
, vol.19
, pp. 1141-1152
-
-
Hamady, M.1
Knight, R.2
-
12
-
-
0000752502
-
The non-concept of species diversity: a critique and alternative parameters
-
Hurlbert, S. H. 1971. The non-concept of species diversity: a critique and alternative parameters. Ecology52, 577-586.
-
(1971)
Ecology
, vol.52
, pp. 577-586
-
-
Hurlbert, S.H.1
-
13
-
-
33845887435
-
GECO - linear visualization for comparative genomics
-
Kuenne, C. T., Ghai, R., Chakraborty, T., and Hain, T. 2007. GECO - linear visualization for comparative genomics. Bioinformatics23, 125-126.
-
(2007)
Bioinformatics
, vol.23
, pp. 125-126
-
-
Kuenne, C.T.1
Ghai, R.2
Chakraborty, T.3
Hain, T.4
-
14
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li, W. and Godzik, A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics22, 1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
15
-
-
0035072551
-
Clustering of highly homologous sequences to reduce the size of large protein databases
-
Li, W., Jaroszewski, L., and Godzik, A. 2001. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics17, 282-283.
-
(2001)
Bioinformatics
, vol.17
, pp. 282-283
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
-
16
-
-
0036699189
-
Sequence clustering strategies improve remote homology recognitions while reducing search times
-
Li, W., Jaroszewski, L., and Godzik, A. 2002. Sequence clustering strategies improve remote homology recognitions while reducing search times. Protein Eng. 15, 643-649.
-
(2002)
Protein Eng.
, vol.15
, pp. 643-649
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
-
17
-
-
54449096251
-
Probing metagenomics by rapid cluster analysis of very large datasets
-
Li, W., Wooley, J. C., and Godzik, A. 2008. Probing metagenomics by rapid cluster analysis of very large datasets. PLoS One3, e3375.
-
(2008)
PLoS One
, vol.3
-
-
Li, W.1
Wooley, J.C.2
Godzik, A.3
-
18
-
-
77956490376
-
Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis
-
Ling, Z., Kong, J., Liu, F., Zhu, H., Chen, X., Wang, Y., Li, L., Nelson, K. E., Xia, Y., and Xiang, C. 2010. Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis. BMC Genomics11, 488.
-
(2010)
BMC Genomics
, vol.11
, pp. 488
-
-
Ling, Z.1
Kong, J.2
Liu, F.3
Zhu, H.4
Chen, X.5
Wang, Y.6
Li, L.7
Nelson, K.E.8
Xia, Y.9
Xiang, C.10
-
19
-
-
72849144434
-
Sequencing technologies - the next generation
-
Metzker, M. L. 2010. Sequencing technologies - the next generation. Nat. Rev. Genet. 11, 31-46.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 31-46
-
-
Metzker, M.L.1
-
20
-
-
0023984847
-
Optimal alignments in linear space
-
Myers, E. W. and Miller, W. 1988. Optimal alignments in linear space. Comput. Appl. Biosci. 4, 11-17.
-
(1988)
Comput. Appl. Biosci.
, vol.4
, pp. 11-17
-
-
Myers, E.W.1
Miller, W.2
-
21
-
-
65949108590
-
Metagenomic pyrosequencing and microbial identification
-
Petrosino, J. F., Highlander, S., Luna, R. A., Gibbs, R. A., and Versalovic, J. 2009. Metagenomic pyrosequencing and microbial identification. Clin. Chem. 55, 856-866.
-
(2009)
Clin. Chem.
, vol.55
, pp. 856-866
-
-
Petrosino, J.F.1
Highlander, S.2
Luna, R.A.3
Gibbs, R.A.4
Versalovic, J.5
-
22
-
-
0033990046
-
Phylogenetic analysis using PHYLIP
-
Retief, J. D. 2000. Phylogenetic analysis using PHYLIP. Methods Mol. Biol. 132, 243-258.
-
(2000)
Methods Mol. Biol.
, vol.132
, pp. 243-258
-
-
Retief, J.D.1
-
23
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., andet al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541.
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
Hollister, E.B.6
Lesniewski, R.A.7
Oakley, B.B.8
Parks, D.H.9
Robinson, C.J.10
-
24
-
-
0027968068
-
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J. D., Higgins, D. G., and Gibson, T. J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
25
-
-
0000770675
-
Report of the ad hoc committee on reconciliation of approaches to bacterial systematics
-
Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E., Stackebrandt, E., andet al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37, 463-464.
-
(1987)
Int. J. Syst. Bacteriol.
, vol.37
, pp. 463-464
-
-
Wayne, L.G.1
Brenner, D.J.2
Colwell, R.R.3
Grimont, P.A.D.4
Kandler, O.5
Krichevsky, M.I.6
Moore, L.H.7
Moore, W.E.C.8
Murray, R.G.E.9
Stackebrandt, E.10
-
26
-
-
77955979374
-
Using affinity propagation combined post-processing to cluster protein sequences
-
Yang, F., Zhu, Q., Tang, D., and Zhao, M. 2009. Using affinity propagation combined post-processing to cluster protein sequences. Protein Pept. Lett. 17, 681-689.
-
(2009)
Protein Pept. Lett.
, vol.17
, pp. 681-689
-
-
Yang, F.1
Zhu, Q.2
Tang, D.3
Zhao, M.4
|