-
1
-
-
0023375315
-
Profile analysis: Detection of distantly related proteins
-
Gribskov, M., McLachlan, A. D., Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A 84, 4355-4358.
-
(1987)
Proc Natl Acad Sci U S A
, vol.84
, pp. 4355-4358
-
-
Gribskov, M.1
McLachlan, A.D.2
Eisenberg, D.3
-
2
-
-
84968924443
-
Protein modeling using hidden Markov models: Analysis of globins
-
Los Alamitos, CA: IEEE Computer Society Press
-
Haussler, D., Krogh, A., Mian, I. S., et al. (1993) Protein modeling using hidden Markov models: analysis of globins, in Proceedings of the Hawaii International Conference on System Sciences. Los Alamitos, CA: IEEE Computer Society Press.
-
(1993)
Proceedings of the Hawaii International Conference on System Sciences
-
-
Haussler, D.1
Krogh, A.2
Mian, I.S.3
-
3
-
-
0030093114
-
A flexible motif search technique based on generalized profiles
-
Bucher, P., Karplus, K., Moeri, N., et al. (1996) A flexible motif search technique based on generalized profiles. Comput Chem 20, 3-23.
-
(1996)
Comput Chem
, vol.20
, pp. 3-23
-
-
Bucher, P.1
Karplus, K.2
Moeri, N.3
-
4
-
-
0000228203
-
A model of evolutionary change in proteins
-
Dayhoff, M, ed, National Biomedical Research Foundation, Washington, DC
-
Dayhoff, M. O., Schwart, R. M., Orcutt, B. C. (1978) A model of evolutionary change in proteins, in (Dayhoff, M., ed.), Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC.
-
(1978)
Atlas of Protein Sequence and Structure
-
-
Dayhoff, M.O.1
Schwart, R.M.2
Orcutt, B.C.3
-
5
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S., Henikoff, J. G. (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 89, 10915-10919.
-
(1992)
Proc Natl Acad Sci U S A
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
6
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman, S. B., Wunsch, C. D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48, 443-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
7
-
-
0000303438
-
The multiple sequence alignment problem in biology
-
Carillo, H., Lipman, D. J. (1988) The multiple sequence alignment problem in biology. SIAM J Appl Math 48, 1073-1082.
-
(1988)
SIAM J Appl Math
, vol.48
, pp. 1073-1082
-
-
Carillo, H.1
Lipman, D.J.2
-
8
-
-
0031458591
-
DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment
-
Stoye, J., Moulton, V., Dress, A. W. (1997) DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. Comput Appl Biosci 13, 625-626.
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 625-626
-
-
Stoye, J.1
Moulton, V.2
Dress, A.W.3
-
9
-
-
0023084055
-
Progressive sequence alignment as a prerequisite to correct phylogenetic trees
-
Feng, D. F., Doolittle, R. F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 25, 351-360.
-
(1987)
J Mol Evol
, vol.25
, pp. 351-360
-
-
Feng, D.F.1
Doolittle, R.F.2
-
10
-
-
0021160693
-
The alignment of sets of sequences and the construction of phyletic trees: An integrated method
-
Hogeweg, P., Hesper, B. (1984) The alignment of sets of sequences and the construction of phyletic trees: an integrated method. J Mol Evol 20, 175-186.
-
(1984)
J Mol Evol
, vol.20
, pp. 175-186
-
-
Hogeweg, P.1
Hesper, B.2
-
11
-
-
0030582739
-
Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
-
Gotoh, O. (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol 264, 823-838.
-
(1996)
J Mol Biol
, vol.264
, pp. 823-838
-
-
Gotoh, O.1
-
12
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., 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
Gish, W.2
Miller, W.3
-
13
-
-
0025272240
-
Rapid and sensitive sequence comparison with FASTP and FASTA
-
Pearson, W. R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183, 63-98.
-
(1990)
Methods Enzymol
, vol.183
, pp. 63-98
-
-
Pearson, W.R.1
-
14
-
-
0030989408
-
Threedimensional domain duplication, swapping and stealing
-
Heringa, J., Taylor, W. R. (1997) Threedimensional domain duplication, swapping and stealing. Curr Opin Struct Biol 7, 416-421.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 416-421
-
-
Heringa, J.1
Taylor, W.R.2
-
15
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T. F., Waterman, M. S. (1981) Identification of common molecular subsequences. J Mol Biol 147, 195-197.
-
(1981)
J Mol Biol
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
16
-
-
0023661088
-
A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons
-
Waterman, M. S., Eggert, M. (1987) A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J Mol Biol 197, 723-728.
-
(1987)
J Mol Biol
, vol.197
, pp. 723-728
-
-
Waterman, M.S.1
Eggert, M.2
-
17
-
-
0032988850
-
BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
-
Thompson, J. D., Plewniak, F., Poch, O. (1999) BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 15, 87-88.
-
(1999)
Bioinformatics
, vol.15
, pp. 87-88
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
18
-
-
0033563413
-
Two strategies for sequence comparison: Profile-preprocessed and secondary structure-induced multiple alignment
-
Heringa, J. (1999) Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment. Comput Chem 23, 341-364.
-
(1999)
Comput Chem
, vol.23
, pp. 341-364
-
-
Heringa, J.1
-
19
-
-
0035984476
-
Local weighting schemes for protein multiple sequence alignment
-
Heringa, J. (2002) Local weighting schemes for protein multiple sequence alignment. Comput Chem 26, 459-477.
-
(2002)
Comput Chem
, vol.26
, pp. 459-477
-
-
Heringa, J.1
-
20
-
-
23144440940
-
PRALINE: A multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
-
Simossis, V. A., Heringa, J. (2005) PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res 33, W289-294.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Simossis, V.A.1
Heringa, J.2
-
21
-
-
0030801002
-
Gapped BLAST and PSIBLAST: A new generation of protein database search programs
-
Altschul, S. F., Madden, T. L., Schaffer, A. A., 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
Schaffer, A.A.3
-
22
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W., Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
23
-
-
0033578684
-
Protein secondary structure prediction based on positionspecific scoring matrices
-
Jones, D. T. (1999) Protein secondary structure prediction based on positionspecific scoring matrices. J Mol Biol 292, 195-202.
-
(1999)
J Mol Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
24
-
-
0027291015
-
Prediction of protein secondary structure at better than 70% accuracy
-
Rost, B., Sander, C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 232, 584-599.
-
(1993)
J Mol Biol
, vol.232
, pp. 584-599
-
-
Rost, B.1
Sander, C.2
-
25
-
-
85142172629
-
-
Lin, K., Simossis, V. A., Taylor, W. Ret al. (2005) A simple and fast secondary structure prediction method using hidden neural networks. Bioinformatics 21, 152-159.
-
Lin, K., Simossis, V. A., Taylor, W. Ret al. (2005) A simple and fast secondary structure prediction method using hidden neural networks. Bioinformatics 21, 152-159.
-
-
-
-
26
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
27
-
-
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
-
28
-
-
1242320272
-
Local homology recognition and distance measures in linear time using compressed amino acid alphabets
-
Edgar, R. C. (2004) Local homology recognition and distance measures in linear time using compressed amino acid alphabets. Nucleic Acids Res 32, 380-385.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 380-385
-
-
Edgar, R.C.1
-
29
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C., Higgins, D. G., Heringa, J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302, 205-217.
-
(2000)
J Mol Biol
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
30
-
-
44949272730
-
A time-efficient, linear-space local similarity algorithm
-
Huang, X., Miller, W. (1991) A time-efficient, linear-space local similarity algorithm. Adv Appl Math 12, 337-357.
-
(1991)
Adv Appl Math
, vol.12
, pp. 337-357
-
-
Huang, X.1
Miller, W.2
-
31
-
-
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., 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
-
32
-
-
2942619012
-
3DCoffee: Combining protein sequences and structures within multiple sequence alignments
-
O'Sullivan, O., Suhre, K., Abergel, C., et al. (2004) 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol 340, 385-395.
-
(2004)
J Mol Biol
, vol.340
, pp. 385-395
-
-
O'Sullivan, O.1
Suhre, K.2
Abergel, C.3
-
33
-
-
0024349252
-
Protein structure alignment
-
Taylor, W. R., Orengo, C. A. (1989) Protein structure alignment. J Mol Biol 208, 1-22.
-
(1989)
J Mol Biol
, vol.208
, pp. 1-22
-
-
Taylor, W.R.1
Orengo, C.A.2
-
34
-
-
0035967880
-
FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi, J., Blundell, T. L., Mizuguchi, K. (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 310, 243-257.
-
(2001)
J Mol Biol
, vol.310
, pp. 243-257
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
35
-
-
33645507429
-
M-Coffee: Combining multiple sequence alignment methods with T-Coffee
-
Wallace, I. M., O'Sullivan, O., Higgins, D. G., et al. (2006) M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res 34, 1692-1699.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 1692-1699
-
-
Wallace, I.M.1
O'Sullivan, O.2
Higgins, D.G.3
-
36
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh, K., Misawa, K., Kuma, K., et al. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30, 3059-3066.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
-
37
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
Katoh, K., Kuma, K., Toh, H., et al. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33, 511-518.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
-
38
-
-
0028787980
-
A weighting system and algorithm for aligning many phylogenetically related sequences
-
Gotoh, O. (1995) A weighting system and algorithm for aligning many phylogenetically related sequences. Comput Appl Biosci 11, 543-551.
-
(1995)
Comput Appl Biosci
, vol.11
, pp. 543-551
-
-
Gotoh, O.1
-
39
-
-
0032126517
-
Generalized affine gap costs for protein sequence alignment
-
Altschul, S. F. (1998) Generalized affine gap costs for protein sequence alignment. Proteins 32, 88-96.
-
(1998)
Proteins
, vol.32
, pp. 88-96
-
-
Altschul, S.F.1
-
40
-
-
11344287710
-
A generalized affine gap model significantly improves protein sequence alignment accuracy
-
Zachariah, M. A., Crooks, G. E., Holbrook, S. R., et al. (2005) A generalized affine gap model significantly improves protein sequence alignment accuracy. Proteins 58, 329-338.
-
(2005)
Proteins
, vol.58
, pp. 329-338
-
-
Zachariah, M.A.1
Crooks, G.E.2
Holbrook, S.R.3
-
41
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
Do, C. B., Mahabhashyam, M. S., Brudno, M., et al. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res 15, 330-340.
-
(2005)
Genome Res
, vol.15
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.2
Brudno, M.3
-
42
-
-
0031721576
-
Dynamic programming alignment accuracy
-
Holmes, I., Durbin, R. (1998) Dynamic programming alignment accuracy. J Comput Biol 5, 493-504.
-
(1998)
J Comput Biol
, vol.5
, pp. 493-504
-
-
Holmes, I.1
Durbin, R.2
-
43
-
-
24644512819
-
SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures
-
Zhou, H., Zhou, Y. (2005) SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics 21, 3615-3621.
-
(2005)
Bioinformatics
, vol.21
, pp. 3615-3621
-
-
Zhou, H.1
Zhou, Y.2
-
44
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost, B. (1999) Twilight zone of protein sequence alignments. Protein Eng 12, 85-94.
-
(1999)
Protein Eng
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
45
-
-
33744782328
-
Global multiple-sequence alignment with repeats
-
Sammeth, M., Heringa, J. (2006) Global multiple-sequence alignment with repeats. Prot Struct Funct Bioinf 64, 263-274.
-
(2006)
Prot Struct Funct Bioinf
, vol.64
, pp. 263-274
-
-
Sammeth, M.1
Heringa, J.2
-
46
-
-
0029861894
-
Multiple DNA and protein sequence alignment based on segment-to-segment comparison
-
Morgenstern, B., Dress, A., Werner, T. (1996) Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc Natl Acad Sci U S A 93, 12098-12103.
-
(1996)
Proc Natl Acad Sci U S A
, vol.93
, pp. 12098-12103
-
-
Morgenstern, B.1
Dress, A.2
Werner, T.3
-
47
-
-
3242891684
-
DIALIGN: Multiple DNA and protein sequence alignment at BiBiServ
-
Morgenstern, B. (2004) DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res 32, W33-36.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Morgenstern, B.1
-
48
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
-
Krogh, A., Larsson, B., von Heijne, G., et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305, 567-580.
-
(2001)
J Mol Biol
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
von Heijne, G.3
-
49
-
-
2142657817
-
A combined transmembrane topology and signal peptide prediction method
-
Kall, L., Krogh, A., Sonnhammer, E.L. (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338, 1027-1036.
-
(2004)
J Mol Biol
, vol.338
, pp. 1027-1036
-
-
Kall, L.1
Krogh, A.2
Sonnhammer, E.L.3
-
50
-
-
1342288004
-
The Jalview Java alignment editor
-
Clamp, M., Cuff, J., Searle, S. M., et al. (2004) The Jalview Java alignment editor. Bioinformatics 20, 426-427.
-
(2004)
Bioinformatics
, vol.20
, pp. 426-427
-
-
Clamp, M.1
Cuff, J.2
Searle, S.M.3
-
51
-
-
0023375195
-
The neighborjoining method: A new method for reconstructing phylogenetic trees
-
Saitou, N., Nei, M. (1987) The neighborjoining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
52
-
-
0030464460
-
SEAVIEW and PHYLO-WIN: Two graphic tools for sequence alignment and molecular phylogeny
-
Galtier, N., Gouy, M., Gautier, C. (1996) SEAVIEW and PHYLO-WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12, 543-548.
-
(1996)
Comput Appl Biosci
, vol.12
, pp. 543-548
-
-
Galtier, N.1
Gouy, M.2
Gautier, C.3
-
54
-
-
85142200589
-
-
Gille, C., Frommel, C. (2001) STRAP: editor for STRuctural Alignments of Proteins. Bioinformatics 17, 377-378.
-
Gille, C., Frommel, C. (2001) STRAP: editor for STRuctural Alignments of Proteins. Bioinformatics 17, 377-378.
-
-
-
-
55
-
-
0032500897
-
-
Parry-Smith, D. J., Payne, A. W., Michie, A. D., et al. (1998) CINEMA-a novel colour INteractive editor for multiple alignments. Gene 221, GC57-63.
-
Parry-Smith, D. J., Payne, A. W., Michie, A. D., et al. (1998) CINEMA-a novel colour INteractive editor for multiple alignments. Gene 221, GC57-63.
-
-
-
-
56
-
-
0030752032
-
Novel developments with the PRINTS protein fingerprint database
-
Attwood, T. K., Beck, M. E., Bleasby, A. J., et al. (1997) Novel developments with the PRINTS protein fingerprint database. Nucleic Acids Res 25, 212-217.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 212-217
-
-
Attwood, T.K.1
Beck, M.E.2
Bleasby, A.J.3
|