-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (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
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
0030801002
-
Gapped BLAST and PSIBLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, SchaÏ ffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSIBLAST: 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
SchaÏ Ffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
3
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85: 2444-2448.
-
(1988)
Proc Natl Acad Sci U S A
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
6
-
-
77956998811
-
The KNDN problem: A quest for unity in diversity
-
Haritsa JR (2009) The KNDN problem: A quest for unity in diversity. IEEE Data Engineering 32: 15-22.
-
(2009)
IEEE Data Engineering
, vol.32
, pp. 15-22
-
-
Haritsa, J.R.1
-
8
-
-
78651319979
-
Ongoing and future developments at the Universal Protein Resource
-
The Uniprot Consortium (2009) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39: 214-219.
-
(2009)
Nucleic Acids Res
, vol.39
, pp. 214-219
-
-
The Uniprot Consortium1
-
9
-
-
10244251690
-
UniProt archive
-
Leinonen R, Diez FG, Binns D, FleischmannW, Lopez R, et al. (2009) UniProt archive. Bioinformatics 20: 3236-3237.
-
(2009)
Bioinformatics
, vol.20
, pp. 3236-3237
-
-
Leinonen, R.1
Diez, F.G.2
Binns, D.3
Fleischmann, W.4
Lopez, R.5
-
10
-
-
34347388470
-
UniRef: Comprehensive and nonredundant UniProt reference clusters
-
Suzek EB, Huang H, McGarvey P, Mazumder R, Wu HC (2007) UniRef: comprehensive and nonredundant UniProt reference clusters. Bioinformatics 23: 1282-1288.
-
(2007)
Bioinformatics
, vol.23
, pp. 1282-1288
-
-
Suzek, E.B.1
Huang, H.2
McGarvey, P.3
Mazumder, R.4
Wu, H.C.5
-
11
-
-
0032642169
-
Winnowing sequences from a database search
-
Berman P, Zhang Z, Wolf YI, Koonin EV, Miller W (1999) Winnowing sequences from a database search. In Proceedings of the Third Annual International Conference on Computational Molecular Biology ACM: 50-58.
-
(1999)
Proceedings of the Third Annual International Conference on Computational Molecular Biology ACM
, pp. 50-58
-
-
Berman, P.1
Zhang, Z.2
Wolf, Y.I.3
Koonin, E.V.4
Miller, W.5
-
12
-
-
0043180474
-
PISCES: A protein sequence culling server
-
Wang G, Dunbrack RL (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591.
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack, R.L.2
-
14
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W, 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
-
-
0036169928
-
Tolerating some redundancy significantly speeds up clustering of large protein databases
-
Li W, Jaroszewski L, Godzik A (2002) Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 18: 77-82.
-
(2002)
Bioinformatics
, vol.18
, pp. 77-82
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
-
16
-
-
0003143622
-
Diversity and dissimilarity coefficients: A unified approach
-
Rao CR (1982) Diversity and dissimilarity coefficients: a unified approach. Theor Popul Biol 21: 24-43.
-
(1982)
Theor Popul Biol
, vol.21
, pp. 24-43
-
-
Rao, C.R.1
-
17
-
-
0034069495
-
Gene ontology: Tool for The Unification of Biology: The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: Tool for The Unification of Biology: The Gene Ontology Consortium. Nature Genetics 25: 25-29.
-
(2000)
Nature Genetics
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
-
18
-
-
0001884644
-
Individual comparisons by ranking methods
-
Wilcoxon F (1945) Individual comparisons by ranking methods. Biometrics Bulletin 6: 80-83
-
(1945)
Biometrics Bulletin
, vol.6
, pp. 80-83
-
-
Wilcoxon, F.1
-
19
-
-
0020848951
-
A survey of recent advances in hierarchical clustering algorithms
-
Murtagh F (1983) A survey of recent advances in hierarchical clustering algorithms. The Computer Journal 26: 354-359.
-
(1983)
The Computer Journal
, vol.26
, pp. 354-359
-
-
Murtagh, F.1
-
20
-
-
33646876613
-
Entropy and diversity
-
Jost L (2006) Entropy and diversity. Oikos 113: 363-375.
-
(2006)
Oikos
, vol.113
, pp. 363-375
-
-
Jost, L.1
-
21
-
-
0026030641
-
Database of homology derived protein structures and the structural meaning of sequence alignment
-
Sander C, Schneider R (1991) Database of homology derived protein structures and the structural meaning of sequence alignment. Proteins: Structure, Function, and Genetics 9: 56-68.
-
(1991)
Proteins: Structure, Function, and Genetics
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
22
-
-
18844397307
-
Measuring diversity from dissimilarities with Rao's quadratic entropy: Are any dissimilarities suitable?
-
Pavoine S, Ollier S, Pontier D (2005) Measuring diversity from dissimilarities with Rao's quadratic entropy: are any dissimilarities suitable? Theor Popul Biol 67: 231-239.
-
(2005)
Theor Popul Biol
, vol.67
, pp. 231-239
-
-
Pavoine, S.1
Ollier, S.2
Pontier, D.3
-
24
-
-
79958017886
-
Toward mechanistic classification of enzyme functions
-
Almonacid D, Babbitt P (2011) Toward mechanistic classification of enzyme functions. Curr Opin Chem Biol 15: 435-442.
-
(2011)
Curr Opin Chem Biol
, vol.15
, pp. 435-442
-
-
Almonacid, D.1
Babbitt, P.2
-
25
-
-
77951557120
-
Nonhomologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution
-
Omelchenko MV, Galperin MY, Wolf YI, Koonin EV (2010) Nonhomologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol Direct 5: 31.
-
(2010)
Biol Direct
, vol.5
, pp. 31
-
-
Omelchenko, M.V.1
Galperin, M.Y.2
Wolf, Y.I.3
Koonin, E.V.4
-
26
-
-
34447294237
-
A new method to measure the semantic similarity of GO terms
-
Wang JZ, Du Z, Payattakool R, Philips SY, Chen CF (2007) A new method to measure the semantic similarity of GO terms. Bioinformatics 23: 1274-1281.
-
(2007)
Bioinformatics
, vol.23
, pp. 1274-1281
-
-
Wang, J.Z.1
Du, Z.2
Payattakool, R.3
Philips, S.Y.4
Chen, C.F.5
-
27
-
-
77954296666
-
A new bioinformatics analysis tools framework at EMBL-EBI
-
Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, et al. (2010) A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res 38: 695-699
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 695-699
-
-
Goujon, M.1
McWilliam, H.2
Li, W.3
Valentin, F.4
Squizzato, S.5
-
29
-
-
2942517966
-
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
-
Raghava GPS, Searle SM, Audley PC, Barber JD, Barton GJ, et al. (2003) OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics 4: 47.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 47
-
-
Raghava, G.P.S.1
Searle, S.M.2
Audley, P.C.3
Barber, J.D.4
Barton, G.J.5
-
31
-
-
77954943853
-
Code optimization of the subroutine to remove near identical matches in sequence database homology search tool PSI-BLAST
-
Aspnä s M, Mattila K, Osowski K, Westerholm J (2010) Code optimization of the subroutine to remove near identical matches in sequence database homology search tool PSI-BLAST. J Comp Biol 17: 819-823.
-
(2010)
J Comp Biol
, vol.17
, pp. 819-823
-
-
Aspnä S, M.1
Mattila, K.2
Osowski, K.3
Westerholm, J.4
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