-
1
-
-
0028679709
-
On the complexity of multiple sequence alignment
-
Wang,L. and Jiang,T. (1994) On the complexity of multiple sequence alignment. J. Comput. Biol., 1, 337-348.
-
(1994)
J. Comput. Biol.
, vol.1
, pp. 337-348
-
-
Wang, L.1
Jiang, T.2
-
2
-
-
0001642687
-
Some biological sequence metrics
-
Waterman,M.S., Smith,T.F. and Beyer,W.A. (1976) Some biological sequence metrics. Adv. Math., 20, 367-387.
-
(1976)
Adv. Math.
, vol.20
, pp. 367-387
-
-
Waterman, M.S.1
Smith, T.F.2
Beyer, W.A.3
-
3
-
-
0021160693
-
The alignment of sets of sequences and the construction of phyletic trees: An integrated method
-
Hogeweg,P. and 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
-
4
-
-
0023084055
-
Progressive sequence alignment as a prerequisite to correct phylogenetic trees
-
Feng,D.F. and 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
-
5
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame,C., Higgins,D.G. and 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
-
6
-
-
0036208872
-
Recent progress in multiple sequence alignment: A survey
-
Notredame,C. (2002) Recent progress in multiple sequence alignment: a survey. Pharmacogenomics, 3, 131-144.
-
(2002)
Pharmacogenomics
, vol.3
, pp. 131-144
-
-
Notredame, C.1
-
7
-
-
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
-
8
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh,K., Misawa,K., Kuma,K. and Miyata,T. (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
Miyata, T.4
-
9
-
-
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
-
12
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou,N. and Nei,M. (1987) The neighbor-joining 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
-
13
-
-
3042550791
-
A comparison of scoring functions for protein sequence profile alignment
-
DOI: 10.1093/bioinformatics/bth090
-
Edgar,R.C. and Sjolander,K. (2004) A comparison of scoring functions for protein sequence profile alignment. Bioinformatics, DOI: 10.1093/bioinformatics/bth090.
-
(2004)
Bioinformatics
-
-
Edgar, R.C.1
Sjolander, K.2
-
14
-
-
0029906607
-
Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology
-
Sjolander,K., Karplus,K., Brown,M., Hughey,R., Krogh,A., Mian,I.S. and Haussler,D. (1996) Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. CABIOS, 12, 327-345.
-
(1996)
CABIOS
, vol.12
, pp. 327-345
-
-
Sjolander, K.1
Karplus, K.2
Brown, M.3
Hughey, R.4
Krogh, A.5
Mian, I.S.6
Haussler, D.7
-
15
-
-
84959053798
-
Improving profile-profile alignment via log average scoring
-
Gascuel,O. and Moret,B.M.E. (eds), Springer-Verlag, Berlin, Germany
-
von Ohsen,N. and Zimmer,R. (2001) Improving profile-profile alignment via log average scoring. In Gascuel,O. and Moret,B.M.E. (eds), Algorithms in Bioinformatics, First International Workshop, WABI 2001. Springer-Verlag, Berlin, Germany, pp. 11-26.
-
(2001)
Algorithms in Bioinformatics, First International Workshop, WABI 2001
, pp. 11-26
-
-
von Ohsen, N.1
Zimmer, R.2
-
16
-
-
0036134748
-
Estimating amino acid substitution models: A comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method
-
Muller,T., Spang,R. and Vingron,M. (2002) Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. Mol. Biol. Evol., 19, 8-13.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 8-13
-
-
Muller, T.1
Spang, R.2
Vingron, M.3
-
17
-
-
0037398368
-
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
-
Brudno,M., Do,C.B., Cooper,G.M., Kim,M.F., Davydov,E., Green,E.D., Sidow,A. and Batzoglou,S. (2003) LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res., 13, 721-731.
-
(2003)
Genome Res.
, vol.13
, pp. 721-731
-
-
Brudno, M.1
Do, C.B.2
Cooper, G.M.3
Kim, M.F.4
Davydov, E.5
Green, E.D.6
Sidow, A.7
Batzoglou, S.8
-
18
-
-
0028928174
-
Comprehensive study on iterative algorithms of multiple sequence alignment
-
Hirosawa,M., Totoki,Y., Hoshida,M. and Ishikawa,M. (1995) Comprehensive study on iterative algorithms of multiple sequence alignment. CABIOS, 11, 13-18.
-
(1995)
CABIOS
, vol.11
, pp. 13-18
-
-
Hirosawa, M.1
Totoki, Y.2
Hoshida, M.3
Ishikawa, M.4
-
19
-
-
0032988850
-
BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
-
Thompson,J.D., Plewniak,F. and Poch,O. (1999a) 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
-
20
-
-
0035175770
-
BAliBASE (Benchmark Alignment dataBASE): Enhancements for repeats, transmembrane sequences and circular permutations
-
Bahr,A., Thompson,J.D., Thierry,J.C. and Poch,O. (2001) BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res., 29, 323-326.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 323-326
-
-
Bahr, A.1
Thompson, J.D.2
Thierry, J.C.3
Poch, O.4
-
21
-
-
3042613056
-
Align-m - A new algorithm for multiple alignment of highly divergent sequences
-
DOI: 10.1093/bioinformatics/bth116
-
Van Walle,I., Lasters,I. and Wyns,L. (2004) Align-m - a new algorithm for multiple alignment of highly divergent sequences. Bioinformatics, DOI: 10.1093/bioinformatics/bth116.
-
(2004)
Bioinformatics
-
-
Van Walle, I.1
Lasters, I.2
Wyns, L.3
-
22
-
-
0032568655
-
SMART, a simple modular architecture research tool: Identification of signaling domains
-
Schultz,J., Milpetz,F., Bork,P. and Ponting,C.P. (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl Acad. Sci. USA, 95, 5857-5864.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 5857-5864
-
-
Schultz, J.1
Milpetz, F.2
Bork, P.3
Ponting, C.P.4
-
23
-
-
0033957469
-
SMART: A web-based tool for the study of genetically mobile domains
-
Schultz,J., Copley,R.R., Doerks,T., Ponting,C.P. and Bork,P. (2000) SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res., 28, 231-234.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 231-234
-
-
Schultz, J.1
Copley, R.R.2
Doerks, T.3
Ponting, C.P.4
Bork, P.5
-
24
-
-
0032919370
-
SMART: Identification and annotation of domains from signalling and extracellular protein sequences
-
Ponting,C.P., Schultz,J., Milpetz,F. and Bork,P. (1999) SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res., 27, 229-332.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 229-332
-
-
Ponting, C.P.1
Schultz, J.2
Milpetz, F.3
Bork, P.4
-
25
-
-
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. and 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
-
-
hompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
26
-
-
0033977581
-
The ASTRAL compendium for protein structure and sequence analysis
-
Brenner,S.E., Koehl,P. and Levitt,M. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 254-256
-
-
Brenner, S.E.1
Koehl, P.2
Levitt, M.3
-
27
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
urzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
28
-
-
0028789439
-
Optimal protein structure alignments by multiple linkage clustering: Application to distantly related proteins
-
Boutonnet,N.S., Rooman,M.J., Ochagavia,M.E., Richelle,J. and Wodak,S.J. (1995) Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins. Protein Eng., 8, 647-662.
-
(1995)
Protein Eng.
, vol.8
, pp. 647-662
-
-
Boutonnet, N.S.1
Rooman, M.J.2
Ochagavia, M.E.3
Richelle, J.4
Wodak, S.J.5
-
29
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
-
(1998)
Protein Eng.
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
30
-
-
0032606140
-
CAFASP-1: Critical assessment of fully automated structure prediction methods
-
Fischer,D., Barret,C., Bryson,K., Elofsson,A., Godzik,A., Jones,D., Karplus,K.J., Kelley,L.A., MacCallum,R.M., Pawowski,K., Rost,B., Rychlewski,L. and Sternberg,M. (1999) CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins, Suppl. 3, 209-217.
-
(1999)
Proteins
, vol.3
, Issue.SUPPL.
, pp. 209-217
-
-
Fischer, D.1
Barret, C.2
Bryson, K.3
Elofsson, A.4
Godzik, A.5
Jones, D.6
Karplus, K.J.7
Kelley, L.A.8
MacCallum, R.M.9
Pawowski, K.10
Rost, B.11
Rychlewski, L.12
Sternberg, M.13
-
31
-
-
0034531045
-
Structure comparison and structure patterns
-
Eidhammer,I., Jonassen,I. and Taylor,W.R. (2000) Structure comparison and structure patterns. J. Comput. Biol., 7, 685-716.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 685-716
-
-
Eidhammer, I.1
Jonassen, I.2
Taylor, W.R.3
-
32
-
-
0034237578
-
Large-scale comparison of protein sequence alignment algorithms with structure alignments
-
Sauder,J.M., Arthur,J.W. and Dunbrack,R.L.,Jr (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins, 40, 6-22.
-
(2000)
Proteins
, vol.40
, pp. 6-22
-
-
Sauder, J.M.1
Arthur, J.W.2
Dunbrack Jr., R.L.3
-
33
-
-
0036211768
-
MaxBench: Evaluation of sequence and structure comparison methods
-
Leplae,R. and Hubbard,T.J. (2002) MaxBench: evaluation of sequence and structure comparison methods. Bioinformatics, 18, 494-495.
-
(2002)
Bioinformatics
, vol.18
, pp. 494-495
-
-
Leplae, R.1
Hubbard, T.J.2
-
34
-
-
0037423702
-
COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
-
Sadreyev,R. and Grishin,N. (2003) COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 317-336
-
-
Sadreyev, R.1
Grishin, N.2
-
35
-
-
2942544229
-
COACH: Profile-profile alignment of protein families using hidden Markov models
-
DOI: 10.1093/bioinformatics/bth091
-
Edgar,R.C. and Sjolander,K. (2004) COACH: profile-profile alignment of protein families using hidden Markov models. Bioinformatics, DOI: 10.1093/bioinformatics/bth091.
-
(2004)
Bioinformatics
-
-
Edgar, R.C.1
Sjolander, K.2
-
36
-
-
0031865006
-
Touring protein fold space with Dali/FSSP
-
Holm,L. and Sander,C. (1998) Touring protein fold space with Dali/FSSP. Nucleic Acids Res., 26, 316-319.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 316-319
-
-
Holm, L.1
Sander, C.2
-
37
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (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
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
38
-
-
0035878724
-
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
-
Schaffer,A.A., Aravind,L., Madden,T.L., Shavirin,S., Spouge,J.L., Wolf,Y.I., Koonin,E.V. and Altschul,S.F. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2994-3005
-
-
Schaffer, A.A.1
Aravind, L.2
Madden, T.L.3
Shavirin, S.4
Spouge, J.L.5
Wolf, Y.I.6
Koonin, E.V.7
Altschul, S.F.8
-
39
-
-
0037251892
-
NCBI Reference Sequence project: Update and current status
-
Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2003) NCBI Reference Sequence project: update and current status. Nucleic Acids Res., 31, 34-37.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 34-37
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
40
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
Thompson,J.D., Plewniak,F. and Poch,O. (1999b) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
41
-
-
3042661708
-
APDB: A novel measure for benchmarking sequence alignment methods without reference alignments
-
O'Sullivan,O., Zehnder,M., Higgins,D., Bucher,P., Grosdidier,A. and Notredame,C. (2003) APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics, 19 Suppl. 1, I215-I221.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
O'Sullivan, O.1
Zehnder, M.2
Higgins, D.3
Bucher, P.4
Grosdidier, A.5
Notredame, C.6
-
42
-
-
84944811700
-
Tbe use of ranks to avoid the assumption of normality implicit in the analysis of variance
-
Friedman,M. (1937) Tbe use of ranks to avoid the assumption of normality implicit in the analysis of variance. J. Am. Stat. Assoc., 32, 675-701.
-
(1937)
J. Am. Stat. Assoc.
, vol.32
, pp. 675-701
-
-
Friedman, M.1
-
43
-
-
0031857684
-
Rose: Generating sequence families
-
Stoye,J., Evers,D. and Meyer,F. (1998) Rose: generating sequence families. Bioinformatics, 14, 157-163.
-
(1998)
Bioinformatics
, vol.14
, pp. 157-163
-
-
Stoye, J.1
Evers, D.2
Meyer, F.3
-
44
-
-
0031604140
-
Phylogenetic inference in protein superfamilies: Analysis of SH2 domains
-
Sjolander,K. (1998) Phylogenetic inference in protein superfamilies: analysis of SH2 domains. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 165-174.
-
(1998)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.6
, pp. 165-174
-
-
Sjolander, K.1
|