-
1
-
-
0025183708
-
Basic local alignment search tool
-
S. F. Altschul, W. Gish, W. Miller, W. Myers, and D. J. Lipman, "Basic local alignment search tool," J. Mol. Bio., 215, pp. 403-410, 1990.
-
(1990)
J. Mol. Bio
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, W.4
Lipman, D.J.5
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, "Gapped BLAST and PSI-BLAST: A new generation of protein database search programs," Nucl. Acids Res., 25, pp. 3389-3402, 1997.
-
(1997)
Nucl. 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
-
3
-
-
0033985049
-
The SYSTERS protein sequence cluster set
-
A. Krause, J. Stoye, and M. Vingron, "The SYSTERS protein sequence cluster set.," Nucl. Acids Res., 28, pp. 270-272, 2000.
-
(2000)
Nucl. Acids Res
, vol.28
, pp. 270-272
-
-
Krause, A.1
Stoye, J.2
Vingron, M.3
-
4
-
-
0346652457
-
ProClust: Improved clustering of protein sequences with an extended graph-based approach
-
P. Pipenbacher, A. Schliep, S. Schneckener, A. Schonhuth, D. Schomburg, and R. Schrader, "ProClust: Improved clustering of protein sequences with an extended graph-based approach," Bioinformatics, 18, pp. S182-S191, 2002.
-
(2002)
Bioinformatics
, vol.18
-
-
Pipenbacher, P.1
Schliep, A.2
Schneckener, S.3
Schonhuth, A.4
Schomburg, D.5
Schrader, R.6
-
5
-
-
0033965852
-
ProtoMap: Automatic classification of protein sequences and hierarchy of protein families
-
G. Yona, N. Linial, and M. Linial, "ProtoMap: Automatic classification of protein sequences and hierarchy of protein families," Nucl. Acids Res., 28, pp. 49-55, 2000.
-
(2000)
Nucl. Acids Res
, vol.28
, pp. 49-55
-
-
Yona, G.1
Linial, N.2
Linial, M.3
-
6
-
-
1042280957
-
Phylogenomic inference of protein molecular function: Advances and challenges
-
K. Sjǒlander, "Phylogenomic inference of protein molecular function: Advances and challenges," Bioinformatics, 20, pp. 170-179, 2000.
-
(2000)
Bioinformatics
, vol.20
, pp. 170-179
-
-
Sjǒlander, K.1
-
8
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
A. J. Enright, S. Van Dongen, and C. A. Ouzounis, "An efficient algorithm for large-scale detection of protein families," Nucl. Acids Res., 30, pp. 1575-1584, 2002.
-
(2002)
Nucl. Acids Res
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
9
-
-
25444458854
-
Super Paramagnetic Clustering of Protein Sequences
-
I. V. Tetko, A. Facius, A. Ruepp, and H. W. Mewes, "Super Paramagnetic Clustering of Protein Sequences," BMC Bioinformatics, 6, pp. 82, 2005.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 82
-
-
Tetko, I.V.1
Facius, A.2
Ruepp, A.3
Mewes, H.W.4
-
10
-
-
47649089645
-
Bioinformatics
-
Cold Spring Harbor Laboratory Press, New York
-
nded.), Cold Spring Harbor Laboratory Press, New York, 2004.
-
(2004)
nded.)
-
-
Mount, D.W.1
-
11
-
-
47649124390
-
-
D. Higgins, Multiple alignment. In The Phylogenetic Handbook. Edited by Salemi M, Vandamme A. M. Cambridge University Press 45, pp 45-71, 2004.
-
D. Higgins, Multiple alignment. In The Phylogenetic Handbook. Edited by Salemi M, Vandamme A. M. Cambridge University Press 45, pp 45-71, 2004.
-
-
-
-
12
-
-
0032891717
-
The transformation distance: A dissimilarity measure based on movements of segments
-
J. S. Varré, J. P. Delahaye, and E. Rivals, "The transformation distance: A dissimilarity measure based on movements of segments," Bioinformatics, 15, pp. 194-202, 1999.
-
(1999)
Bioinformatics
, vol.15
, pp. 194-202
-
-
Varré, J.S.1
Delahaye, J.P.2
Rivals, E.3
-
13
-
-
25444461672
-
Scoredist: A simple and robust sequence distance estimator
-
E. L. L. Sonnhammer, and V. Hollich, "Scoredist: A simple and robust sequence distance estimator," BMC Bioinformatics, 6, pp 108, 2005.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 108
-
-
Sonnhammer, E.L.L.1
Hollich, V.2
-
14
-
-
0034125366
-
Probabilistic and statistical properties of words: An overview
-
G. Reinert, S. Schbath, and M. S. Waterman, "Probabilistic and statistical properties of words: An overview," J. Comp. Biol., 7, pp. 1-46, 2000.
-
(2000)
J. Comp. Biol
, vol.7
, pp. 1-46
-
-
Reinert, G.1
Schbath, S.2
Waterman, M.S.3
-
15
-
-
1242320272
-
Local homology recognition and distance measures in linear time using compressed amino acid alphabets
-
R. C. Edgar, "Local homology recognition and distance measures in linear time using compressed amino acid alphabets," Nucl. Acids Res., 32, pp. 380-385, 2004.
-
(2004)
Nucl. Acids Res
, vol.32
, pp. 380-385
-
-
Edgar, R.C.1
-
16
-
-
0014421064
-
Evolutionary rate at the molecular level
-
M. Kimura, "Evolutionary rate at the molecular level. Nature," 217, pp. 624-626, 1968.
-
(1968)
Nature
, vol.217
, pp. 624-626
-
-
Kimura, M.1
-
17
-
-
0031084471
-
An alternating least squares approach to inferring phylogenies from pairwise distances
-
J. Felsenstein, "An alternating least squares approach to inferring phylogenies from pairwise distances," Syst. Biol., 46, pp. 101, 1997.
-
(1997)
Syst. Biol
, vol.46
, pp. 101
-
-
Felsenstein, J.1
-
18
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
S. Henikoff, and J. G. Henikoff, "Amino acid substitution matrices from protein blocks," Proceedings of the National Academy of Sciences of the United States of America,"89, pp. 10915-10919, 1992.
-
(1992)
Proceedings of the National Academy of Sciences of the United States of America
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
19
-
-
0000228203
-
A model of evolutionary change in proteins
-
M. O. Dayhoff, R. M. Schwartz, and B. C. Orcutt, "A model of evolutionary change in proteins," Atlas of Protein Sequence and Structure, vol. 5, suppl. 3, pp. 345-352, 1978.
-
(1978)
Atlas of Protein Sequence and Structure
, vol.5
, Issue.SUPPL. 3
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
20
-
-
2742569191
-
Comparative statistics for DNA and protein sequences: Single sequence analysis
-
S. Karlin, and G. Ghandour, "Comparative statistics for DNA and protein sequences: Single sequence analysis," Proc. Natl. Acad. Sci. USA, 82, pp. 5800-5804, 1985.
-
(1985)
Proc. Natl. Acad. Sci. USA
, vol.82
, pp. 5800-5804
-
-
Karlin, S.1
Ghandour, G.2
-
21
-
-
84944178665
-
Hierarchical Grouping to Optimize an Objective Function
-
J. H. Ward, "Hierarchical Grouping to Optimize an Objective Function," J. Am. Stat. Assoc. 58, pp. 236-244, 1963.
-
(1963)
J. Am. Stat. Assoc
, vol.58
, pp. 236-244
-
-
Ward, J.H.1
-
22
-
-
84977007441
-
Application of a Hierarchical Grouping Procedure to a Problem of Grouping Profiles
-
J. H. Ward, and M. E. Hook, "Application of a Hierarchical Grouping Procedure to a Problem of Grouping Profiles," Educ. Psychol. Meas,, 23, pp. 69-82, 1963.
-
(1963)
Educ. Psychol. Meas
, vol.23
, pp. 69-82
-
-
Ward, J.H.1
Hook, M.E.2
-
23
-
-
0003922190
-
-
John Wiley and Sons
-
R. O. Duda, P. E. Hart, and D. G. Stork, "Pattern Classification, second edition," John Wiley and Sons, 2001.
-
(2001)
Pattern Classification, second edition
-
-
Duda, R.O.1
Hart, P.E.2
Stork, D.G.3
-
24
-
-
0028013177
-
Improved sensitivity of profile searches through the use of sequence weights and gap excision
-
J. D. Thompson, D. G. Higgins, and T. J. Gibson, "Improved sensitivity of profile searches through the use of sequence weights and gap excision," Comput. Appl. Biosci., 10, pp. 19-29, 1994.
-
(1994)
Comput. Appl. Biosci
, vol.10
, pp. 19-29
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
25
-
-
10644276935
-
Generalized Ward and related clustering problems
-
edited by H. H. Bock, Amsterdam: Elsevier, pp
-
V. Batagelj, Generalized Ward and related clustering problems. In Classification and Related Methods of Data Analysis, edited by H. H. Bock, Amsterdam: Elsevier, pp. 67-74, 1998.
-
(1998)
Classification and Related Methods of Data Analysis
, pp. 67-74
-
-
Batagelj, V.1
-
26
-
-
0034897827
-
Secator: A Program for Inferring Protein Subfamilies from Phylogenetic Trees
-
N. Wicker, G. R. Perrin, J. C. Thierry, and O. Poch, "Secator: A Program for Inferring Protein Subfamilies from Phylogenetic Trees," Mol. Biol. Evol., 18, pp. 1435-1441, 2001.
-
(2001)
Mol. Biol. Evol
, vol.18
, pp. 1435-1441
-
-
Wicker, N.1
Perrin, G.R.2
Thierry, J.C.3
Poch, O.4
-
28
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
J. D. Thompson, D. G. Higgins, and T. J. Gibson, "CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice," Nucl. Acids Res., 22, pp. 4673-4680, 1994.
-
(1994)
Nucl. Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
30
-
-
0003422388
-
-
5th ed. New York and Basingstoke: W.H. Freeman and Co
-
H. Lodish, A. Berk, P. Matsudaira, C. A. Kaiser, M. Krieger, M. P. Scott, L. Zipursky and J. Darnell, Molecular Cell Biology, 5th ed. New York and Basingstoke: W.H. Freeman and Co., 2004.
-
(2004)
Molecular Cell Biology
-
-
Lodish, H.1
Berk, A.2
Matsudaira, P.3
Kaiser, C.A.4
Krieger, M.5
Scott, M.P.6
Zipursky, L.7
Darnell, J.8
-
32
-
-
33645010330
-
Two exo-β-D-glucosaminidases/ exochitosanases from actinomycetes define a new subfamily within family 2 of glycoside hydrolases
-
N. Côté, A. Fleury, E. Dumont-Blanchette, T. Fukamizo, M. Mitsutomi, and R. Brzezinski, "Two exo-β-D-glucosaminidases/ exochitosanases from actinomycetes define a new subfamily within family 2 of glycoside hydrolases," Biochem. J., 394, pp. 675-686, 2006.
-
(2006)
Biochem. J
, vol.394
, pp. 675-686
-
-
Côté, N.1
Fleury, A.2
Dumont-Blanchette, E.3
Fukamizo, T.4
Mitsutomi, M.5
Brzezinski, R.6
-
33
-
-
33749556013
-
Exo-β-D-glucosaminidase from Amycolatopsis orientalis: Catalytic residues, sugar recognition specificity, kinetics, and synergism
-
T. Fukamizo, A. Fleury, N. Côté, M. Mitsutomi, and R. Brzezinski, "Exo-β-D-glucosaminidase from Amycolatopsis orientalis: Catalytic residues, sugar recognition specificity, kinetics, and synergism," Glycobiology, 16, pp. 1064-1072, 2006.
-
(2006)
Glycobiology
, vol.16
, pp. 1064-1072
-
-
Fukamizo, T.1
Fleury, A.2
Côté, N.3
Mitsutomi, M.4
Brzezinski, R.5
-
34
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
R. C. Edgar, "MUSCLE: A multiple sequence alignment method with reduced time and space complexity," BMC Bioinformatics, 5, pp. 113, 2004.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
35
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
K. Katoh, K. Misawa, K. Kuma, and T. Miyata, "MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform," Nucl. Acids Res., 30, pp. 3059-3066, 2002.
-
(2002)
Nucl. Acids Res
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
Miyata, T.4
-
36
-
-
0034623005
-
T-Coffee: A novel method for multiple sequence alignments
-
C. Notredame, D. Higgins, and J. Heringa, "T-Coffee: A novel method for multiple sequence alignments," Journal of Molecular Biology, 302, pp. 205-217, 2000.
-
(2000)
Journal of Molecular Biology
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.2
Heringa, J.3
|