-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F. et al. (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
-
3
-
-
27144489108
-
Protein database searches using compositionally adjusted substitution matrices
-
Altschul, S. F. et al. (2005) Protein database searches using compositionally adjusted substitution matrices. FEBS J., 272, 5101-5109.
-
(2005)
FEBS J.
, vol.272
, pp. 5101-5109
-
-
Altschul, S.F.1
-
4
-
-
84879920277
-
Compressive genomics for protein databases
-
Daniels, N. M. et al. (2013) Compressive genomics for protein databases. Bioinformatics, 29, i283-i290.
-
(2013)
Bioinformatics
, vol.29
, pp. i283-i290
-
-
Daniels, N.M.1
-
5
-
-
75549090603
-
The pfam protein families database
-
Finn, R. D. et al. (2010) The pfam protein families database. Nucleic Acids Res., 38 (Suppl. 1), D211-D222.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. D211-D222
-
-
Finn, R.D.1
-
6
-
-
84870431038
-
CD-HIT: Accelerated for clustering the next-generation sequencing data
-
Fu, L. et al. (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28, 3150-3152.
-
(2012)
Bioinformatics
, vol.28
, pp. 3150-3152
-
-
Fu, L.1
-
7
-
-
80052722544
-
Meeting report: The terabase metagenomics workshop and the vision of an Earth microbiome project
-
Gilbert, J. A. et al. (2010) Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand. Genomic Sci., 3, 243-248.
-
(2010)
Stand. Genomic Sci.
, vol.3
, pp. 243-248
-
-
Gilbert, J.A.1
-
8
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent, W. J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
9
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
Kurokawa, K. et al. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res., 14, 169-181.
-
(2007)
DNA Res.
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
-
10
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. and Salzberg, S. L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
11
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
-
12
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
13
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
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. Bioinformatics, 22, 1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
15
-
-
0027681165
-
Suffix arrays: A new method for on-line string searches
-
Manber, U. and Myers, G. (1993) Suffix arrays: a new method for on-line string searches. SIAM J. Comput., 22, 935-948.
-
(1993)
SIAM J. Comput.
, vol.22
, pp. 935-948
-
-
Manber, U.1
Myers, G.2
-
16
-
-
33646808944
-
Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets
-
Melo, F. and Marti-Renom, M. A. (2006) Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets. Proteins, 63, 986-995.
-
(2006)
Proteins
, vol.63
, pp. 986-995
-
-
Melo, F.1
Marti-Renom, M.A.2
-
17
-
-
0001338954
-
Simplified amino acid alphabets for protein fold recognition and implications for folding
-
Murphy, L. R. et al. (2000) Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng., 13, 149-152.
-
(2000)
Protein Eng.
, vol.13
, pp. 149-152
-
-
Murphy, L.R.1
-
18
-
-
0025950944
-
Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
-
Pearson, W. R. (1991) Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics, 11, 635-650.
-
(1991)
Genomics
, vol.11
, pp. 635-650
-
-
Pearson, W.R.1
-
19
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J. et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59-65.
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
-
20
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov, R. L. et al. (1997) A genomic perspective on protein families. Science, 278, 631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
-
21
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
Tatusov, R. L. et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
-
22
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
The Human Microbiome Project Consortium
-
The Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207-214.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
23
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
Turnbaugh, P. J. et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444, 1027-1031.
-
(2006)
Nature
, vol.444
, pp. 1027-1031
-
-
Turnbaugh, P.J.1
-
24
-
-
78651415181
-
GPU-BLAST: Using graphics processors to accelerate protein sequence alignment
-
Vouzis, P. D. and Sahinidis, N. V. (2011) GPU-BLAST: using graphics processors to accelerate protein sequence alignment. Bioinformatics, 27, 182-188.
-
(2011)
Bioinformatics
, vol.27
, pp. 182-188
-
-
Vouzis, P.D.1
Sahinidis, N.V.2
-
25
-
-
79955877212
-
RAPSearch: A fast protein similarity search tool for short reads
-
Ye, Y. et al. (2011) RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics, 12, 159.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 159
-
-
Ye, Y.1
-
26
-
-
84855167751
-
RAPSearch2: A fast and memory-efficient protein similarity search tool for next-generation sequencing data
-
Zhao, Y. et al. (2012) RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics, 28, 125-126.
-
(2012)
Bioinformatics
, vol.28
, pp. 125-126
-
-
Zhao, Y.1
|