-
1
-
-
33744811392
-
Multiple sequence alignment
-
DOI 10.1016/j.sbi.2006.04.004, PII S0959440X06000704
-
Edgar, R.C. and Batzoglou, S.: Multiple sequence alignment, Curr Opin Struct Biol, Vol.16, No.3, pp.368-373 (2006). (Pubitemid 43831644)
-
(2006)
Current Opinion in Structural Biology
, vol.16
, Issue.3
, pp. 368-373
-
-
Edgar, R.C.1
Batzoglou, S.2
-
2
-
-
0032789448
-
Multiple sequence alignment: Algorithms and applications
-
DOI 10.1016/S0065-227X(99)80007-0
-
Gotoh, O.: Multiple sequence alignment: Algorithms and applications, Adv Biophys, Vol.36, pp.159-206 (1999). (Pubitemid 29344450)
-
(1999)
Advances in Biophysics
, vol.36
, pp. 159-206
-
-
Gotoh, O.1
-
3
-
-
0036208872
-
Recent progress in multiple sequence alignment: A survey
-
DOI 10.1517/14622416.3.1.131
-
Notredame, C.: Recent progress in multiple sequence alignment: A survey, Pharmacogenomics, Vol.3, No.1, pp.131-144 (2002). (Pubitemid 34285245)
-
(2002)
Pharmacogenomics
, vol.3
, Issue.1
, pp. 131-144
-
-
Notredame, C.1
-
4
-
-
34548400364
-
Recent evolutions of multiple sequence alignment algorithms
-
Notredame, C.: Recent evolutions of multiple sequence alignment algorithms, PLoS Comput Biol, Vol.3, No.8, p.e123 (2007).
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.8
-
-
Notredame, C.1
-
5
-
-
85145635935
-
-
Aluru, S. (Ed.) Chapman & Hall/CRC
-
Gotoh, O., Yamada, S. and Yada, T.: Multiple sequence alignment, Handbook of computational molecular biology, Aluru, S. (Ed.), Chapman & Hall/CRC, pp.3-1- 3-36 (2005).
-
(2005)
Multiple Sequence Alignment, Handbook of Computational Molecular Biology
, pp. 31-336
-
-
Gotoh, O.1
Yamada, S.2
Yada, T.3
-
6
-
-
14544303948
-
-
Jiang, T., Xu, Y. and Zhang, M.Q. (Eds.), Tsinghua University Press
-
Jiang, T. and Wang, L.: Algorithmic methods for multiple sequence alignment, Current topics in computational molecular biology, Jiang, T., Xu, Y. and Zhang, M.Q. (Eds.), Tsinghua University Press (2002).
-
(2002)
Algorithmic Methods for Multiple Sequence Alignment, Current Topics in Computational Molecular Biology
-
-
Jiang, T.1
Wang, L.2
-
7
-
-
3543097981
-
Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
-
DOI 10.1093/bioinformatics/bth126
-
Grasso, C. and Lee, C.: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems, Bioinformatics, Vol.20, No.10, pp.1546-1556 (2004). (Pubitemid 39023158)
-
(2004)
Bioinformatics
, vol.20
, Issue.10
, pp. 1546-1556
-
-
Grasso, C.1
Lee, C.2
-
8
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C., Higgins, D.G. and Heringa, J.: T-Coffee: A novel method for fast and accurate multiple sequence alignment, J Mol Biol, Vol.302, No.1, pp.205-217 (2000).
-
(2000)
J Mol Biol
, vol.302
, Issue.1
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
9
-
-
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.: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res, Vol.22, No.22, pp.4673-4680 (1994). (Pubitemid 24354800)
-
(1994)
Nucleic Acids Research
, vol.22
, Issue.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
10
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
DOI 10.1093/nar/gkh340
-
Edgar, R.C.: MUSCLE: Multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, Vol.32, No.5, pp.1792-1797 (2004). (Pubitemid 38832724)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
11
-
-
0030582739
-
Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
-
DOI 10.1006/jmbi.1996.0679
-
Gotoh, O.: Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments, J Mol Biol, Vol.264, No.4, pp.823-838 (1996). (Pubitemid 27013563)
-
(1996)
Journal of Molecular Biology
, vol.264
, Issue.4
, pp. 823-838
-
-
Gotoh, O.1
-
12
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh, K., Misawa, K., Kuma, K. and Miyata, T.: MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Res, Vol.30, No.14, pp.3059-3066 (2002). (Pubitemid 34851225)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.14
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.-I.3
Miyata, T.4
-
13
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
DOI 10.1093/nar/gki198
-
Katoh, K., Kuma, K., Toh, H. andMiyata, T.:MAFFT version 5: Improvement in accuracy of multiple sequence alignment, Nucleic Acids Res, Vol.33, No.2, pp.511- 518 (2005). (Pubitemid 40360980)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.2
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.-I.2
Toh, H.3
Miyata, T.4
-
14
-
-
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. and Yamana, Y.: Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost, BMC Bioinformatics, Vol.7, p.524 (2006).
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 524
-
-
Yamada, S.1
Gotoh, O.2
Yamana, Y.3
-
15
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar, R.C.: MUSCLE: A multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, Vol.5, p.113 (2004).
-
(2004)
BMC Bioinformatics
, Issue.5
, pp. 113
-
-
Edgar, R.C.1
-
16
-
-
34547756442
-
Automatic extraction of reliable regions from multiple sequence alignments
-
Lassmann, T. and Sonnhammer, E.: Automatic extraction of reliable regions from multiple sequence alignments, BMC Bioinformatics, Vol.8, p.S9 (2007).
-
(2007)
BMC Bioinformatics
, vol.8
-
-
Lassmann, T.1
Sonnhammer, E.2
-
17
-
-
0038391401
-
RASCAL: Rapid scanning and correction of multiple sequence alignments
-
DOI 10.1093/bioinformatics/btg133
-
Thompson, J.D., Thierry, J.C. and Poch, O.: RASCAL: Rapid scanning and correction of multiple sequence alignments, Bioinformatics, Vol.19, No.9, pp.1155-1161 (2003). (Pubitemid 36790019)
-
(2003)
Bioinformatics
, vol.19
, Issue.9
, pp. 1155-1161
-
-
Thompson, J.D.1
Thierry, J.C.2
Poch, O.3
-
18
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
DOI 10.1101/gr.2821705
-
Do, C.B., Mahabhashyam, M.S.P., Brudno, M. and Batzoglou, S.: ProbCons: Probabilistic consistency-based multiple sequence alignment, Genome Res, Vol.15, No.2, pp.330-340 (2005). (Pubitemid 40309398)
-
(2005)
Genome Research
, vol.15
, Issue.2
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.P.2
Brudno, M.3
Batzoglou, S.4
-
19
-
-
33645507429
-
M-Coffee: Combining multiple sequence alignment methods with T-Coffee
-
Wallace, I., O'Sullivan, O., Higgins, D.G. and Notredame, C.: M-Coffee: Combining multiple sequence alignment methods with T-Coffee, Nucleic Acids Res, Vol.34, No.6, pp.1692-1699 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.6
, pp. 1692-1699
-
-
Wallace, I.1
O'Sullivan, O.2
Higgins, D.G.3
Notredame, C.4
-
20
-
-
2942619012
-
3DCoffee: Combining protein sequences and structures within multiple sequence alignments
-
DOI 10.1016/j.jmb.2004.04.058, PII S0022283604005212
-
O'Sullivan, O., Suhre, K., Abergel, C., Higgins, D.G. and Notredame, C.: 3DCoffee: Combining protein sequences and structures within multiple sequence alignments, J Mol Biol, Vol.340, No.2, pp.385-395 (2004). (Pubitemid 38759917)
-
(2004)
Journal of Molecular Biology
, vol.340
, Issue.2
, pp. 385-395
-
-
O'Sullivan, O.1
Suhre, K.2
Abergel, C.3
Higgins, D.G.4
Notredame, C.5
-
21
-
-
33750001271
-
MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information
-
DOI 10.1093/nar/gkl514
-
Pei, J. and Grishin, N.: MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information, Nucleic Acids Res, Vol.34, No.16, pp.4364-4374 (2006). (Pubitemid 44567036)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.16
, pp. 4364-4374
-
-
Pei, J.1
Grishin, N.V.2
-
22
-
-
24644512819
-
SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures
-
DOI 10.1093/bioinformatics/bti582
-
Zhou, H. and Zhou, Y.: SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures, Bioinformatics, Vol.21, No.18, pp.3615-3621 (2005). (Pubitemid 41264096)
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3615-3621
-
-
Zhou, H.1
Zhou, Y.2
-
23
-
-
34548390530
-
-
DeCaprio, D., Vinson, J., Pearson, M., Montgomery, P., Doherty, M. and Galagan, J.: Conrad: Gene prediction using conditional random fields, Genome Res, Vol.17, No.9, pp.1389-1398 (2007).
-
(2007)
Conrad: Gene prediction using conditional random fields, Genome Res
, vol.17
, Issue.9
, pp. 1389-1398
-
-
DeCaprio, D.1
Vinson, J.2
Pearson, M.3
Montgomery, P.4
Doherty, M.5
Galagan, J.6
-
24
-
-
33847262911
-
Robust prediction of consensus secondary structures using averaged base pairing probability matrices
-
DOI 10.1093/bioinformatics/btl636
-
Kiryu, H., Kin, T. and Asai, K.: Robust prediction of consensus secondary structures using averaged base pairing probability matrices, Bioinformatics, Vol.23, No.4, pp.434-441 (2007). (Pubitemid 46323124)
-
(2007)
Bioinformatics
, vol.23
, Issue.4
, pp. 434-441
-
-
Kiryu, H.1
Kin, T.2
Asai, K.3
-
25
-
-
0024985346
-
Optimal sequence alignment allowing for long gaps
-
Gotoh, O.: Optimal sequence alignment allowing for long gaps, Bull Math Biol, Vol.52, No.3, pp.359-373 (1990).
-
(1990)
Bull Math Biol
, vol.52
, Issue.3
, pp. 359-373
-
-
Gotoh, O.1
-
26
-
-
0020484488
-
An improved algorithm for matching biological sequences
-
Gotoh, O.: An improved algorithm for matching biological sequences, J Mol Biol, Vol.162, No.3, pp.705-708 (1982).
-
(1982)
J Mol Biol
, vol.162
, Issue.3
, pp. 705-708
-
-
Gotoh, O.1
-
27
-
-
0027210418
-
Optimal alignment between groups of sequences and its application to multiple sequence alignment
-
Gotoh, O.: Optimal alignment between groups of sequences and its application to multiple sequence alignment, Comput Appl Biosci, Vol.9, No.3, pp.361-370 (1993). (Pubitemid 23193511)
-
(1993)
Computer Applications in the Biosciences
, vol.9
, Issue.3
, pp. 361-370
-
-
Gotoh, O.1
-
28
-
-
0028041177
-
Further improvement in methods of group-to-group sequence alignment with generalized profile operations
-
Gotoh, O.: Further improvement in methods of group-to-group sequence alignment with generalized profile operations, Comput Appl Biosci, Vol.10, No.4, pp.379-387 (1994). (Pubitemid 24267491)
-
(1994)
Computer Applications in the Biosciences
, vol.10
, Issue.4
, pp. 379-387
-
-
Gotoh, O.1
-
29
-
-
0029595355
-
A reliable sequence alignment method based on probabilities of residue correspondences
-
Miyazawa, S.: A reliable sequence alignment method based on probabilities of residue correspondences, Protein Eng, Vol.8, No.10, pp.999-1009 (1995). (Pubitemid 26008492)
-
(1995)
Protein Engineering
, vol.8
, Issue.10
, pp. 999-1009
-
-
Miyazawa, S.1
-
30
-
-
0003516147
-
-
Cambridge University Press
-
Durin, R., Eddy, S.R., Krogh, A. and Mitchison, G.: Biological sequence analysis, Cambridge University Press (1998).
-
(1998)
Biological Sequence Analysis
-
-
Durin, R.1
Eddy, S.R.2
Krogh, A.3
Mitchison, G.4
-
31
-
-
20444489707
-
DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment
-
Subramanian, A.R., Weyer-Menkhoff, J., Kaufmann, M. and Morgenstern, B.: DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment, BMC Bioinformatics, Vol.6, p.66 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 66
-
-
Subramanian, A.R.1
Weyer-Menkhoff, J.2
Kaufmann, M.3
Morgenstern, B.4
-
32
-
-
0032988850
-
BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
-
DOI 10.1093/bioinformatics/15.1.87
-
Thompson, J.D., Plewniak, F. and Poch, O.: BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs, Bioinformatics, Vol.15, No.1, pp.87-88 (1999). (Pubitemid 29101202)
-
(1999)
Bioinformatics
, vol.15
, Issue.1
, pp. 87-88
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
33
-
-
0035175770
-
BAliBASE (Benchmark Alignment dataBASE): Enhancements for repeats, transmembrane sequences and circular permutations
-
Bahr, A., Thompson, J., Thierry, J. and Poch, O.: BAliBASE (Benchmark Alignment dataBASE): Enhancements for repeats, transmembrane sequences and circular permutations, Nucleic Acids Res, Vol.29, No.1, pp.323-326 (2001). (Pubitemid 32054482)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.1
, pp. 323-326
-
-
Bahr, A.1
Thompson, J.D.2
Thierry, J.-C.3
Poch, O.4
-
34
-
-
24644457706
-
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
-
DOI 10.1002/prot.20527
-
Thompson, J.D., Koehl, P., Ripp, R. and Poch, O.: BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark, Proteins, Vol.61, No.1, pp.127-136 (2005). (Pubitemid 41263414)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.61
, Issue.1
, pp. 127-136
-
-
Thompson, J.D.1
Koehl, P.2
Ripp, R.3
Poch, O.4
-
35
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
DOI 10.1093/nar/27.13.2682
-
Thompson, J.D., Plewniak, F. and Poch, O.: A comprehensive comparison of multiple sequence alignment programs, Nucleic Acids Res, Vol.27, No.13, pp.2682-2690 (1999). (Pubitemid 29306566)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.13
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
|