-
1
-
-
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., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 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
-
2
-
-
0034777598
-
Clustering protein sequences -structure prediction by transitive homology
-
Bolten, E., Schliep, A., Schneckener, S., Schomburg, D., Schrader, R.: Clustering protein sequences -structure prediction by transitive homology. Bioinformatics 17 (2001) 935-941
-
(2001)
Bioinformatics
, vol.17
, pp. 935-941
-
-
Bolten, E.1
Schliep, A.2
Schneckener, S.3
Schomburg, D.4
Schrader, R.5
-
3
-
-
0033006303
-
Combining many multiple alignments in one improved alignment
-
Bucka-Lassen, K., Caprani, O., Hein, J.: Combining many multiple alignments in one improved alignment. Bioinformatics 15 (1999) 122-130
-
(1999)
Bioinformatics
, vol.15
, pp. 122-130
-
-
Bucka-Lassen, K.1
Caprani, O.2
Hein, J.3
-
4
-
-
33745783706
-
CONTRAlign: Discriminative training for protein sequence alignment
-
Do, C.B., Gross, S.S., Batzoglou, S.: CONTRAlign: discriminative training for protein sequence alignment. Lect. Notes Bioinformatics 3909 (2006) 160-174
-
(2006)
Lect. Notes Bioinformatics
, vol.3909
, pp. 160-174
-
-
Do, C.B.1
Gross, S.S.2
Batzoglou, S.3
-
5
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
Do, C.B., Mahabhashyam, M.S., Brudno, M., Batzoglou, S.: ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res. 15 (2005) 330-340
-
(2005)
Genome Res
, vol.15
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.2
Brudno, M.3
Batzoglou, S.4
-
6
-
-
0003516147
-
-
Cambridge University Press
-
Durbin, R., Eddy, S., Krogh, A., Mitchison, G.: Biological sequence analysis. Cambridge University Press (1998)
-
(1998)
Biological sequence analysis
-
-
Durbin, R.1
Eddy, S.2
Krogh, A.3
Mitchison, G.4
-
7
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar, R.C.: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 (2004) 1792-1797
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
8
-
-
3042550791
-
A comparison of scoring functions for protein sequence profile alignment
-
Edgar, R.C., Sjölander, K.: A comparison of scoring functions for protein sequence profile alignment. Bioinformatics 20 (2004) 1301-1308
-
(2004)
Bioinformatics
, vol.20
, pp. 1301-1308
-
-
Edgar, R.C.1
Sjölander, K.2
-
9
-
-
0031762837
-
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence
-
Gerstein, M.: Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. Bioinformatics 14 (1998) 707-714
-
(1998)
Bioinformatics
, vol.14
, pp. 707-714
-
-
Gerstein, M.1
-
10
-
-
0030582739
-
Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
-
Gotoh, O.: Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol. 264 (1996) 823-838
-
(1996)
J. Mol. Biol
, vol.264
, pp. 823-838
-
-
Gotoh, O.1
-
11
-
-
0027351056
-
Efficient methods for multiple sequence alignment with guaranteed error bounds
-
Gusfield, D.: Efficient methods for multiple sequence alignment with guaranteed error bounds. Bull. Math. Biol. 55 (1993) 141-154
-
(1993)
Bull. Math. Biol
, vol.55
, pp. 141-154
-
-
Gusfield, D.1
-
12
-
-
8444243745
-
Accurate detection of very sparse sequence motifs
-
Heger, A., Lappe, M., Holm, L.: Accurate detection of very sparse sequence motifs. J. Comp. Biol. 11 (2004) 843-857
-
(2004)
J. Comp. Biol
, vol.11
, pp. 843-857
-
-
Heger, A.1
Lappe, M.2
Holm, L.3
-
13
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones, D.T.: Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292 (1999) 195-202
-
(1999)
J. Mol. Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
14
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
Katoh, K., Kuma, K., Toh, H., Miyata, T.: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33 (2005) 511-518
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
15
-
-
29244447181
-
Kalign -an accurate and fast multiple sequence alignment algorithm
-
Lassmann, T., Sonnharnmer, E.L.L.: Kalign -an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6 (2005) 298
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 298
-
-
Lassmann, T.1
Sonnharnmer, E.L.L.2
-
16
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
Lee, C., Grasso, C., Sharlow, M.F.: Multiple sequence alignment using partial order graphs. Bioinformatics 18 (2002) 452-464
-
(2002)
Bioinformatics
, vol.18
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
17
-
-
0036169928
-
Tolerating some redundancy significantly speeds up clustering of large protein databases
-
Li, W., Jaroszewski, L., Godzik, A.: Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 18 (2002) 77-82
-
(2002)
Bioinformatics
, vol.18
, pp. 77-82
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
-
18
-
-
0034491129
-
Saturated BLAST: An automated multiple intermediate sequence search used to detect distant homology
-
Li, W., Pio, F., Pawlowski, K., Godzik, A.: Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics 16 (2000) 1105-1110
-
(2000)
Bioinformatics
, vol.16
, pp. 1105-1110
-
-
Li, W.1
Pio, F.2
Pawlowski, K.3
Godzik, A.4
-
19
-
-
25444458541
-
PSI-BLAST-ISS: An intermediate sequence search tool for estimation of the position-specific alignment reliability
-
Margelevic̀ius, M., Venclovas, C.: PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability. BMC Bioinformatics 6 (2005) 185
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 185
-
-
Margelevic̀ius, M.1
Venclovas, C.2
-
20
-
-
1842559320
-
Alignment of protein sequences by their profiles
-
Marti-Renom, M.A., Madhusudhan, M.S., Sali, A.: Alignment of protein sequences by their profiles. Protein Sci. 13 (2004) 1071-1087
-
(2004)
Protein Sci
, vol.13
, pp. 1071-1087
-
-
Marti-Renom, M.A.1
Madhusudhan, M.S.2
Sali, A.3
-
21
-
-
0031766401
-
HOMSTRAD: A database of protein structure alignments for homologous families
-
Mizuguchi, K., Deane, C.M., Blundell, T.L., Overington, J.P.: HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci. 7 (1998) 2469-2471
-
(1998)
Protein Sci
, vol.7
, pp. 2469-2471
-
-
Mizuguchi, K.1
Deane, C.M.2
Blundell, T.L.3
Overington, J.P.4
-
22
-
-
0029861894
-
Multiple DNA and protein sequence alignment based on segment-to-segment comparison
-
Morgenstern, B., Dress, A., Werner, T.: Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. USA 93 (1996) 12098-12103
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 12098-12103
-
-
Morgenstern, B.1
Dress, A.2
Werner, T.3
-
23
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C., Higgins, D.G., Heringa, J.: T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302 (2000) 205-217
-
(2000)
J. Mol. Biol
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
24
-
-
2942619012
-
3DCoffee: Combining protein sequences and structures within multiple sequence alignments
-
O'Sullivan, O., Suhre, K., Abergel, C., Higgins, D.G., Notredame, C: 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol. 340 (2004) 385-395
-
(2004)
J. Mol. Biol
, vol.340
, pp. 385-395
-
-
O'Sullivan, O.1
Suhre, K.2
Abergel, C.3
Higgins, D.G.4
Notredame, C.5
-
25
-
-
0031576361
-
Intermediate sequences increase the detection of homology between sequences
-
Park, J., Teichmann, S.A., Hubbard, T., Chothia, C.: Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol. 273 (1997) 349-354
-
(1997)
J. Mol. Biol
, vol.273
, pp. 349-354
-
-
Park, J.1
Teichmann, S.A.2
Hubbard, T.3
Chothia, C.4
-
26
-
-
33750001271
-
MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information
-
Pei, J., Grishin, N.V.: MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res. 34 (2006) 4364-4374
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 4364-4374
-
-
Pei, J.1
Grishin, N.V.2
-
27
-
-
33751004142
-
Probalign: Multiple sequence alignment using partition function posterior probabilities
-
Roshan, U., Livesay, D.R.: Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics 22 (2006) 2715-2721
-
(2006)
Bioinformatics
, vol.22
, pp. 2715-2721
-
-
Roshan, U.1
Livesay, D.R.2
-
28
-
-
0032940341
-
Combining sensitive database searches with multiple intermediates to detect distant homologues
-
Salamov, A.A., Suwa, M., Orengo, C.A., Swindells, M.B.: Combining sensitive database searches with multiple intermediates to detect distant homologues. Protein Eng. 12 (1999) 95-100
-
(1999)
Protein Eng
, vol.12
, pp. 95-100
-
-
Salamov, A.A.1
Suwa, M.2
Orengo, C.A.3
Swindells, M.B.4
-
29
-
-
13844311019
-
Homology-extended sequence alignment
-
Simossis, V.A., Kleinjung, J., Heringa, J.: Homology-extended sequence alignment. Nucleic Acids Res. 33 (2005) 816-824
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 816-824
-
-
Simossis, V.A.1
Kleinjung, J.2
Heringa, J.3
-
30
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. J. Mol. Biol. 147 (1981) 195-197
-
(1981)
J. Mol. Biol
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
31
-
-
0345676554
-
Multiple sequence alignment with the divide-and-conquer method
-
Stoye, J.: Multiple sequence alignment with the divide-and-conquer method. Gene 211 (1998) GC45-56
-
(1998)
Gene
, vol.211
-
-
Stoye, J.1
-
32
-
-
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.: 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 (1994) 4673-4680
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
33
-
-
24644457706
-
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
-
Thompson, J.D., Koehl, P., Ripp, R., Poch, O.: BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins 61 (2005) 127-136
-
(2005)
Proteins
, vol.61
, pp. 127-136
-
-
Thompson, J.D.1
Koehl, P.2
Ripp, R.3
Poch, O.4
-
34
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
Thompson, J.D., Plewniak, F., Poch, O.: A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 27 (1999) 2682-2690
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
35
-
-
3042613056
-
Align-m - a new algorithm for multiple alignment of highly divergent sequences
-
Van Walle, L., Lasters, I., Wyns, L.: Align-m - a new algorithm for multiple alignment of highly divergent sequences. Bioinformatics 20 (2004) 1428-1435
-
(2004)
Bioinformatics
, vol.20
, pp. 1428-1435
-
-
Van Walle, L.1
Lasters, I.2
Wyns, L.3
-
36
-
-
33645507429
-
M-Coffee: Combining multiple sequence alignment methods with T-Coffee
-
Wallace, I.M., O'Sullivan, O., Higgins, D.G., Notredame, C.: M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 34 (2006) 1692-1699
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 1692-1699
-
-
Wallace, I.M.1
O'Sullivan, O.2
Higgins, D.G.3
Notredame, C.4
-
37
-
-
78651011426
-
Probability tables for individual comparisons by ranking methods
-
Wilcoxon, F.: Probability tables for individual comparisons by ranking methods. Biometrics 3 (1947) 119-122
-
(1947)
Biometrics
, vol.3
, pp. 119-122
-
-
Wilcoxon, F.1
-
38
-
-
33846581070
-
Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost
-
Yamada, S., Gotoh, O., Yamana, H.: Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost. BMC Bioinformatics 7 (2006) 524
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 524
-
-
Yamada, S.1
Gotoh, O.2
Yamana, H.3
-
39
-
-
24644512819
-
SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures
-
Zhou, H., Zhou, Y.: SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics 21 (2005) 3615-3621
-
(2005)
Bioinformatics
, vol.21
, pp. 3615-3621
-
-
Zhou, H.1
Zhou, Y.2
|