-
1
-
-
0001213953
-
Simultaneous comparison of three or more sequences related by a tree, time warps, string edits and macromolecules
-
Addison-Wesley, Reading, MA
-
Sankoff D, Cedergren RJ (1983) Simultaneous comparison of three or more sequences related by a tree, time warps, string edits and macromolecules. The theory and practice of sequence comparison. Addison-Wesley, Reading, MA, pp 253-263
-
(1983)
The Theory and Practice of Sequence Comparison
, pp. 253-263
-
-
Sankoff, D.1
Cedergren, R.J.2
-
2
-
-
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
-
3
-
-
0023084055
-
Progressive sequence alignment as a prerequisite to correct phylogenetic trees
-
Feng DF, Doolittle RF (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
-
4
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ (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
-
5
-
-
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
-
6
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame C, Higgins DG, 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
-
7
-
-
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
-
8
-
-
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
-
9
-
-
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
-
10
-
-
3042550791
-
A comparison of scoring functions for protein sequence profile alignment
-
Edgar RC, Sjölander K (2004) A comparison of scoring functions for protein sequence profile alignment. Bioinformatics 20: 1301-1308
-
(2004)
Bioinformatics
, vol.20
, pp. 1301-1308
-
-
Edgar, R.C.1
Sjölander, K.2
-
11
-
-
2442663920
-
Scoring profile-to-profile sequence alignments
-
Wang G, Dunbrack RL Jr (2004) Scoring profile-to-profile sequence alignments. Protein Sci 13:1612-1626
-
(2004)
Protein Sci
, vol.13
, pp. 1612-1626
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
12
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915-10919
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
14
-
-
0029046744
-
An assessment of amino acid exchange matrices in aligning protein sequences: The twilight zone revisited
-
Vogt G, Etzold T, Argos P (1995) An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. J Mol Biol 249:816-831
-
(1995)
J Mol Biol
, vol.249
, pp. 816-831
-
-
Vogt, G.1
Etzold, T.2
Argos, P.3
-
15
-
-
14144256112
-
Comparison of protein sequences and practical database searching
-
Higgins D, Taylor W (eds) Oxford University Press, New York
-
Yona G, Brenner SE (2000) Comparison of protein sequences and practical database searching. In: Higgins D, Taylor W (eds) Bioinformatics: sequence, structure, and databanks. A practical approach. Oxford University Press, New York, pp 167-190
-
(2000)
Bioinformatics: Sequence, Structure, and Databanks. A Practical Approach
, pp. 167-190
-
-
Yona, G.1
Brenner, S.E.2
-
16
-
-
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
-
17
-
-
0346734129
-
The compositional adjustment of amino acid substitution matrices
-
Yu Y-K, Wootton JC, Altschul SF (2003) The compositional adjustment of amino acid substitution matrices. Proc Natl Acad Sci 100: 15688-15693
-
(2003)
Proc Natl Acad Sci
, vol.100
, pp. 15688-15693
-
-
Yu, Y.-K.1
Wootton, J.C.2
Altschul, S.F.3
-
19
-
-
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 9:56-68
-
(1991)
Proteins
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
20
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826
-
(1986)
EMBO J
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
21
-
-
9544241332
-
The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods
-
Simossis VA, Heringa J (2004) The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods. Comput Biol Chem 28:351-366
-
(2004)
Comput Biol Chem
, vol.28
, pp. 351-366
-
-
Simossis, V.A.1
Heringa, J.2
-
22
-
-
0034334542
-
Computational methods for protein secondary structure prediction using multiple sequence alignments
-
Heringa J (2000) Computational methods for protein secondary structure prediction using multiple sequence alignments. Curr Protein Pept Sci 1:273-301
-
(2000)
Curr Protein Pept Sci
, vol.1
, pp. 273-301
-
-
Heringa, J.1
-
23
-
-
13244255462
-
Protein family comparison using statistical models and predicted structural information
-
Chung R, Yona G (2004) Protein family comparison using statistical models and predicted structural information. BMC Bioinformatics 5:183
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 183
-
-
Chung, R.1
Yona, G.2
-
24
-
-
0042121000
-
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure
-
Ginalski K, Pas J, Wyrwicz LS et al (2003) ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res 31:3804-3807
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3804-3807
-
-
Ginalski, K.1
Pas, J.2
Wyrwicz, L.S.3
-
25
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Söding, J.1
-
26
-
-
4143083332
-
Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures
-
vonOhsen N, Sommer I, Zimmer R et al (2004) Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics 20:2228-2235
-
(2004)
Bioinformatics
, vol.20
, pp. 2228-2235
-
-
Vonohsen, N.1
Sommer, I.2
Zimmer, R.3
-
28
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195-202
-
(1999)
J Mol Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
29
-
-
0036568279
-
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
-
Pollastri G, Przybylski D, Rost B et al (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47:228-235
-
(2002)
Proteins
, vol.47
, pp. 228-235
-
-
Pollastri, G.1
Przybylski, D.2
Rost, B.3
-
30
-
-
17444397116
-
Porter: A new, accurate server for protein secondary structure prediction
-
Pollastri G, McLysaght A (2005) Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics 21:1719-1720
-
(2005)
Bioinformatics
, vol.21
, pp. 1719-1720
-
-
Pollastri, G.1
McLysaght, A.2
-
31
-
-
13444266488
-
A simple and fast secondary structure prediction method using hidden neural networks
-
Lin K, Simossis VA, Taylor WR et al (2005) A simple and fast secondary structure prediction method using hidden neural networks. Bioinformatics 21:152-159
-
(2005)
Bioinformatics
, vol.21
, pp. 152-159
-
-
Lin, K.1
Simossis, V.A.2
Taylor, W.R.3
-
33
-
-
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
-
34
-
-
0025997601
-
Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities
-
Luthy R, McLachlan AD, Eisenberg D (1991) Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins 10:229-239
-
(1991)
Proteins
, vol.10
, pp. 229-239
-
-
Luthy, R.1
McLachlan, A.D.2
Eisenberg, D.3
-
35
-
-
0028153788
-
A mutation data matrix for transmembrane proteins
-
Jones DT, Taylor WR, Thornton JM (1994) A mutation data matrix for transmembrane proteins. FEBS Lett 339:269-275
-
(1994)
FEBS Lett
, vol.339
, pp. 269-275
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
36
-
-
1842559800
-
STAM: Simple transmembrane alignment method
-
Shafrir Y, Guy HR (2004) STAM: simple transmembrane alignment method. Bioinformatics 20:758-769
-
(2004)
Bioinformatics
, vol.20
, pp. 758-769
-
-
Shafrir, Y.1
Guy, H.R.2
-
37
-
-
39149144057
-
PRALINETM: A strategy for improved multiple alignment of transmembrane proteins
-
Pirovano W, Feenstra KA, Heringa J (2008) PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. Bioinformatics 24:492-497
-
(2008)
Bioinformatics
, vol.24
, pp. 492-497
-
-
Pirovano, W.1
Feenstra, K.A.2
Heringa, J.3
-
38
-
-
2142657817
-
A combined transmembrane topology and signal peptide prediction method
-
Kall L, Krogh A, Sonnhammer ELL (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.L.3
-
39
-
-
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
-
40
-
-
0034786532
-
The HMMTOP transmembrane topology prediction server
-
Tusnády GE, Simon I (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17:849-850
-
(2001)
Bioinformatics
, vol.17
, pp. 849-850
-
-
Tusnády, G.E.1
Simon, I.2
-
41
-
-
0033670313
-
PHAT: A transmembrane-specific substitution matrix
-
Ng PC, Henikoff JG, Henikoff S (2000) PHAT: a transmembrane-specific substitution matrix. Bioinformatics 16:760-766
-
(2000)
Bioinformatics
, vol.16
, pp. 760-766
-
-
Ng, P.C.1
Henikoff, J.G.2
Henikoff, S.3
-
42
-
-
0028928174
-
Comprehensive study on iterative algorithms of multiple sequence alignment
-
Hirosawa M, Totoki Y, HoshidaMet al (1995) Comprehensive study on iterative algorithms of multiple sequence alignment. Comput Appl Biosci 11:13-18
-
(1995)
Comput Appl Biosci
, vol.11
, pp. 13-18
-
-
Hirosawa, M.1
Totoki, Y.2
Hoshida, M.3
-
43
-
-
13244255415
-
MUSCLE: Amultiple sequence alignment method with reduced time and space complexity
-
EdgarRC(2004)MUSCLE: amultiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
44
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC (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
-
45
-
-
0033990061
-
Flexible sequence similarity searching with the FASTA3 program package
-
Pearson WR
-
Pearson WR (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 132:185-219
-
(2000)
Methods Mol Biol
, vol.132
, pp. 185-219
-
-
-
46
-
-
0026656815
-
Exhaustive matching of the entire protein sequence database
-
Gonnet GH, Cohen MA, Benner SA (1992) Exhaustive matching of the entire protein sequence database. Science 256:1443-1445
-
(1992)
Science
, vol.256
, pp. 1443-1445
-
-
Gonnet, G.H.1
Cohen, M.A.2
Benner, S.A.3
-
47
-
-
24644457706
-
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
-
Thompson JD, Koehl P, Ripp R et al (2005) BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins 61:127-136
-
(2005)
Proteins
, vol.61
, pp. 127-136
-
-
Thompson, J.D.1
Koehl, P.2
Ripp, R.3
-
48
-
-
33744782328
-
Global multiple-sequence alignment with repeats
-
Sammeth M, Heringa J (2006) Global multiple-sequence alignment with repeats. Proteins 64:263-274
-
(2006)
Proteins
, vol.64
, pp. 263-274
-
-
Sammeth, M.1
Heringa, J.2
|