-
1
-
-
27544471726
-
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap
-
10.1093/bioinformatics/bti627, 16105900
-
Price GA, Crooks GE, Green RE, Brenner SE. Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. Bioinformatics 2005, 21:3824-31. 10.1093/bioinformatics/bti627, 16105900.
-
(2005)
Bioinformatics
, vol.21
, pp. 3824-3831
-
-
Price, G.A.1
Crooks, G.E.2
Green, R.E.3
Brenner, S.E.4
-
2
-
-
0027968068
-
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
10.1093/nar/22.22.4673, 308517, 7984417
-
Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-80. 10.1093/nar/22.22.4673, 308517, 7984417.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
3
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
10.1101/gr.2821705, 546535, 15687296
-
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res 2005, 15:330-40. 10.1101/gr.2821705, 546535, 15687296.
-
(2005)
Genome Res
, vol.15
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.2
Brudno, M.3
Batzoglou, S.4
-
4
-
-
33747874580
-
CONTRAfold: RNA secondary structure prediction without physics-based models
-
10.1093/bioinformatics/btl246, 16873527
-
Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 2006, 22:e90-8. 10.1093/bioinformatics/btl246, 16873527.
-
(2006)
Bioinformatics
, vol.22
-
-
Do, C.B.1
Woods, D.A.2
Batzoglou, S.3
-
6
-
-
55949093159
-
Learning scoring schemes for sequence alignment from partial examples
-
10.1109/TCBB.2008.57, 18989042
-
Kim E, Kececioglu J. Learning scoring schemes for sequence alignment from partial examples. IEEE/ACM Trans Comput Biol Bioinform 2008, 5:546-56. 10.1109/TCBB.2008.57, 18989042.
-
(2008)
IEEE/ACM Trans Comput Biol Bioinform
, vol.5
, pp. 546-556
-
-
Kim, E.1
Kececioglu, J.2
-
7
-
-
0026736581
-
Parametric sequence comparisons
-
10.1073/pnas.89.13.6090, 49443, 1631095
-
Waterman MS, Eggert M, Lander E. Parametric sequence comparisons. Proc Natl Acad Sci USA 1992, 89:6090-3. 10.1073/pnas.89.13.6090, 49443, 1631095.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 6090-6093
-
-
Waterman, M.S.1
Eggert, M.2
Lander, E.3
-
8
-
-
33745584089
-
Parametric alignment of Drosophila genomes
-
10.1371/journal.pcbi.0020073, 1480539,1480539, 16789815
-
Dewey CN, Huggins PM, Woods K, Sturmfels B, Pachter L. Parametric alignment of Drosophila genomes. PLoS Comput Biol 2006, 2:e73. 10.1371/journal.pcbi.0020073, 1480539,1480539, 16789815.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Dewey, C.N.1
Huggins, P.M.2
Woods, K.3
Sturmfels, B.4
Pachter, L.5
-
10
-
-
84858770497
-
Tighter bounds for structured estimation
-
Chapelle O, Do C, Le Q, Smola A, Teo C. Tighter bounds for structured estimation. Proc NIPS 2009 2009,
-
(2009)
Proc NIPS 2009
-
-
Chapelle, O.1
Do, C.2
Le, Q.3
Smola, A.4
Teo, C.5
-
11
-
-
70349215207
-
Automatic parameter learning for multiple local network alignment
-
10.1089/cmb.2009.0099, 19645599
-
Flannick J, Novak A, Do CB, Srinivasan BS, Batzoglou S. Automatic parameter learning for multiple local network alignment. J Comput Biol 2009, 16:1001-22. 10.1089/cmb.2009.0099, 19645599.
-
(2009)
J Comput Biol
, vol.16
, pp. 1001-1022
-
-
Flannick, J.1
Novak, A.2
Do, C.B.3
Srinivasan, B.S.4
Batzoglou, S.5
-
12
-
-
13744252890
-
MAFFT version 5: improvement in accuracy of multiple sequence alignment
-
10.1093/nar/gki198, 548345, 15661851
-
Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005, 33:511-8. 10.1093/nar/gki198, 548345, 15661851.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
13
-
-
33748940447
-
Analysis and comparison of benchmarks for multiple sequence alignment
-
Blackshields G, Wallace IM, Larkin M, Higgins DG. Analysis and comparison of benchmarks for multiple sequence alignment. In Silico Biol 2006, 6:321-39.
-
(2006)
In Silico Biol
, vol.6
, pp. 321-339
-
-
Blackshields, G.1
Wallace, I.M.2
Larkin, M.3
Higgins, D.G.4
-
14
-
-
0032988850
-
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
-
10.1093/bioinformatics/15.1.87, 10068696
-
Thompson JD, Plewniak F, Poch O. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 1999, 15:87-8. 10.1093/bioinformatics/15.1.87, 10068696.
-
(1999)
Bioinformatics
, vol.15
, pp. 87-88
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
15
-
-
0242712166
-
Non-Linear optimisation techniques
-
Oliver & Boyd
-
Box M, Davies D, Swann W. Non-Linear optimisation techniques. 1969, Oliver & Boyd.
-
(1969)
-
-
Box, M.1
Davies, D.2
Swann, W.3
-
16
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
10.1073/pnas.89.22.10915, 50453, 1438297
-
Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992, 89:10915-9. 10.1073/pnas.89.22.10915, 50453, 1438297.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
17
-
-
40449129755
-
BLOSUM62 miscalculations improve search performance
-
10.1038/nbt0308-274, 18327232
-
Styczynski MP, Jensen KL, Rigoutsos I, Stephanopoulos G. BLOSUM62 miscalculations improve search performance. Nat Biotechnol 2008, 26:274-5. 10.1038/nbt0308-274, 18327232.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 274-275
-
-
Styczynski, M.P.1
Jensen, K.L.2
Rigoutsos, I.3
Stephanopoulos, G.4
-
18
-
-
0003552989
-
Atlas of Protein Sequence and Structure
-
Washington: N.B.R.F
-
Dayhoff MO. Atlas of Protein Sequence and Structure. 1978, Washington: N.B.R.F.
-
(1978)
-
-
Dayhoff, M.O.1
-
19
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8:275-82.
-
(1992)
Comput Appl Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
20
-
-
0036134748
-
Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method
-
Muller T, Spang R, Vingron M. Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. Mol Biol Evol 2002, 19:8-13.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 8-13
-
-
Muller, T.1
Spang, R.2
Vingron, M.3
-
21
-
-
0034922289
-
Modeling amino acid replacement
-
10.1089/10665270050514918, 11382360
-
Muller T, Vingron M. Modeling amino acid replacement. J Comput Biol 2000, 7:761-76. 10.1089/10665270050514918, 11382360.
-
(2000)
J Comput Biol
, vol.7
, pp. 761-776
-
-
Muller, T.1
Vingron, M.2
-
22
-
-
0030013081
-
Blocks database and its applications
-
full_text, 8743679
-
Henikoff JG, Henikoff S. Blocks database and its applications. Methods Enzymol 1996, 266:88-105. full_text, 8743679.
-
(1996)
Methods Enzymol
, vol.266
, pp. 88-105
-
-
Henikoff, J.G.1
Henikoff, S.2
-
23
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
10.1093/nar/gkh340, 390337, 15034147
-
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-7. 10.1093/nar/gkh340, 390337, 15034147.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
24
-
-
29244447181
-
Kalign--an accurate and fast multiple sequence alignment algorithm
-
10.1186/1471-2105-6-298, 1325270, 16343337
-
Lassmann T, Sonnhammer EL. Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 2005, 6:298. 10.1186/1471-2105-6-298, 1325270, 16343337.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 298
-
-
Lassmann, T.1
Sonnhammer, E.L.2
-
25
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
10.1093/bioinformatics/btm404, 17846036
-
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-8. 10.1093/bioinformatics/btm404, 17846036.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
26
-
-
13244255415
-
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
-
10.1186/1471-2105-5-113, 517706, 15318951
-
Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5:113. 10.1186/1471-2105-5-113, 517706, 15318951.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
27
-
-
33845682909
-
Multiple alignment of protein sequences with repeats and rearrangements
-
10.1093/nar/gkl511, 1635250, 17068081
-
Phuong TM, Do CB, Edgar RC, Batzoglou S. Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Res 2006, 34:5932-42. 10.1093/nar/gkl511, 1635250, 17068081.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 5932-5942
-
-
Phuong, T.M.1
Do, C.B.2
Edgar, R.C.3
Batzoglou, S.4
-
28
-
-
3042613056
-
Align-m--a new algorithm for multiple alignment of highly divergent sequences
-
10.1093/bioinformatics/bth116, 14962914
-
Van Walle I, Lasters I, Wyns L. Align-m--a new algorithm for multiple alignment of highly divergent sequences. Bioinformatics 2004, 20:1428-35. 10.1093/bioinformatics/bth116, 14962914.
-
(2004)
Bioinformatics
, vol.20
, pp. 1428-1435
-
-
Van Walle, I.1
Lasters, I.2
Wyns, L.3
-
29
-
-
0026656815
-
Exhaustive matching of the entire protein sequence database
-
10.1126/science.1604319, 1604319
-
Gonnet GH, Cohen MA, Benner SA. Exhaustive matching of the entire protein sequence database. Science 1992, 256:1443-5. 10.1126/science.1604319, 1604319.
-
(1992)
Science
, vol.256
, pp. 1443-1445
-
-
Gonnet, G.H.1
Cohen, M.A.2
Benner, S.A.3
-
30
-
-
33750001271
-
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information
-
10.1093/nar/gkl514, 1636350, 16936316
-
Pei J, Grishin NV. MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res 2006, 34:4364-74. 10.1093/nar/gkl514, 1636350, 16936316.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 4364-4374
-
-
Pei, J.1
Grishin, N.V.2
|