-
1
-
-
0028679709
-
On the complexity of multiple sequence alignment
-
Wang L and Jiang T. On the complexity of multiple sequence alignment. Journal of computational biology, 1(4):337-348, 1994.
-
(1994)
Journal of Computational Biology
, vol.1
, Issue.4
, pp. 337-348
-
-
Wang, L.1
Jiang, T.2
-
2
-
-
34548400364
-
Recent evolutions of multiple sequence alignment algorithms
-
Notredame C. Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol, 3(8):e123, 2007.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.8
-
-
Notredame, C.1
-
3
-
-
0023084055
-
Progressive sequence alignment as a prerequisite to correct phylogenetic trees
-
Feng DF and Doolittle RF. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Journal of molecular evolution, 25(4):351-360, 1987.
-
(1987)
Journal of Molecular Evolution
, vol.25
, Issue.4
, pp. 351-360
-
-
Feng, D.F.1
Doolittle, R.F.2
-
4
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame C, Higgins DG, and Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302(1):205-217, 2000.
-
(2000)
Journal of Molecular Biology
, vol.302
, Issue.1
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
5
-
-
0031829993
-
COFFEE: An objective function for multiple sequence alignments
-
Notredame C, Holm L, and Higgins DG. COFFEE: an objective function for multiple sequence alignments. Bioinformatics, 14(5):407-422, 1998.
-
(1998)
Bioinformatics
, vol.14
, Issue.5
, pp. 407-422
-
-
Notredame, C.1
Holm, L.2
Higgins, D.G.3
-
6
-
-
0029887381
-
Hidden Markov models for sequence analysis: Extension and analysis of the basic method
-
April
-
Hughey R and Krogh A. Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci, 12(2):95-107, April 1996.
-
(1996)
Comput Appl Biosci
, vol.12
, Issue.2
, pp. 95-107
-
-
Hughey, R.1
Krogh, A.2
-
7
-
-
77955034236
-
Cloud-Coffee: Implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud
-
08
-
Di Tommaso P, Orobitg M, Guirado F, Cores F, Espinosa T, and Notredame C. Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud. Bioinformatics, 26(15):1903-1904, 08 2010.
-
(2010)
Bioinformatics
, vol.26
, Issue.15
, pp. 1903-1904
-
-
Di Tommaso, P.1
Orobitg, M.2
Guirado, F.3
Cores, F.4
Espinosa, T.5
Notredame, C.6
-
8
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
March
-
Needleman S and Wunsch C. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48(3):443-453, March 1970.
-
(1970)
Journal of Molecular Biology
, vol.48
, Issue.3
, pp. 443-453
-
-
Needleman, S.1
Wunsch, C.2
-
9
-
-
0019887799
-
Identification of common molecular subsequences
-
March
-
Smith TF and Waterman MS. Identification of common molecular subsequences. Journal of molecular biology, 147(1):195-197, March 1981.
-
(1981)
Journal of Molecular Biology
, vol.147
, Issue.1
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
10
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson J, Higgins D, and Gibson T. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22):4673-4680, 1994.
-
(1994)
Nucleic Acids Research
, vol.22
, Issue.22
, pp. 4673-4680
-
-
Thompson, J.1
Higgins, D.2
Gibson, T.3
-
11
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
Katoh K, Kuma K-I, Toh H, and Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research, 33(2):511-518, 2005.
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.2
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.-I.2
Toh, H.3
Miyata, T.4
-
12
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5):1792-1797, 2004.
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
13
-
-
0032945593
-
DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
-
Morgenstern B. DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15(3):211-218, 1999.
-
(1999)
Bioinformatics
, vol.15
, Issue.3
, pp. 211-218
-
-
Morgenstern, B.1
-
14
-
-
45949105543
-
DIALIGN-TX: Greedy and progressive approaches for segment-based multiple sequence alignment
-
Subramanian AR, Kaufmann M, and Morgenstern B. DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms for Molecular Biology, 3(6), 2008.
-
(2008)
Algorithms for Molecular Biology
, vol.3
, pp. 6
-
-
Subramanian, A.R.1
Kaufmann, M.2
Morgenstern, B.3
-
15
-
-
80054078476
-
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
-
October
-
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soding J, Thompson JD, and Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7(1), October 2011.
-
(2011)
Molecular Systems Biology
, vol.7
, Issue.1
-
-
Sievers, F.1
Wilm, A.2
Dineen, D.3
Gibson, T.J.4
Karplus, K.5
Li, W.6
Lopez, R.7
McWilliam, H.8
Remmert, M.9
Soding, J.10
Thompson, J.D.11
Higgins, D.G.12
-
17
-
-
84944719946
-
FastLSA: A fast, linear-space, parallel and sequential algorithm for sequence alignment
-
oct.
-
Driga A, Lu P, Schaeffer J, Szafron D, Charter K, and Parsons I. FastLSA: a fast, linear-space, parallel and sequential algorithm for sequence alignment. In Parallel Processing, 2003. Proceedings. 2003 International Conference on, pages 48-57, oct. 2003.
-
(2003)
Parallel Processing, 2003. Proceedings. 2003 International Conference on
, pp. 48-57
-
-
Driga, A.1
Lu, P.2
Schaeffer, J.3
Szafron, D.4
Charter, K.5
Parsons, I.6
-
18
-
-
46149108116
-
Z-align: An Exact and Parallel Strategy for Local Biological Sequence Alignment in User-Restricted Memory Space
-
Sept.
-
Batista RB and Alves de Melo ACM. Z-align: An Exact and Parallel Strategy for Local Biological Sequence Alignment in User-Restricted Memory Space. In Cluster Computing, 2006 IEEE International Conference on, pages 1-10, Sept. 2006.
-
(2006)
Cluster Computing, 2006 IEEE International Conference on
, pp. 1-10
-
-
Batista, R.B.1
Alves De Melo, A.C.M.2
-
19
-
-
11044228089
-
Space and Time Optimal Parallel Sequence Alignments
-
Dec.
-
Rajko S and Aluru S. Space and Time Optimal Parallel Sequence Alignments. IEEE Trans. Parallel Distrib. Syst., 15:1070-1081, Dec. 2004.
-
(2004)
IEEE Trans. Parallel Distrib. Syst.
, vol.15
, pp. 1070-1081
-
-
Rajko, S.1
Aluru, S.2
-
20
-
-
0041386069
-
ClustalW-MPI: ClustalW analysis using distributed and parallel computing
-
08
-
Li K-B. ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics, 19(12):1585-1586, 08 2003.
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1585-1586
-
-
Li, K.-B.1
-
21
-
-
84925520830
-
Parallel-TCoffee: A parallel multiple sequence aligner
-
Zola J, Yang X, Rospondek S, and Aluru S. Parallel-TCoffee: A parallel multiple sequence aligner. In ISCA PDCS-2007, pages 248-253, 2007.
-
(2007)
ISCA PDCS-2007
, pp. 248-253
-
-
Zola, J.1
Yang, X.2
Rospondek, S.3
Aluru, S.4
-
22
-
-
13244259261
-
Fast pair-wise and multiple sequence alignment using parallel processors
-
Schmollinger M, Nieselt K, Kaufmann M, and Morgenstern B. DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors. BMC Bioinformatics, 5(1):128, 2004.
-
(2004)
BMC Bioinformatics
, vol.5
, Issue.1
, pp. 128
-
-
Schmollinger, M.1
Nieselt, K.2
Kaufmann, M.3
Morgenstern, B.4
Dialign, P.5
-
23
-
-
0022150790
-
Allocating Independent Subtasks on Parallel Processors
-
Oct.
-
Kruskal CP and Weiss A. Allocating Independent Subtasks on Parallel Processors. Software Engineering, IEEE Transactions on, SE-11(10):1001-1016, Oct. 1985.
-
(1985)
Software Engineering, IEEE Transactions on
, vol.SE-11
, Issue.10
, pp. 1001-1016
-
-
Kruskal, C.P.1
Weiss, A.2
-
24
-
-
0023535689
-
Guided Self-Scheduling: A Practical Scheduling Scheme for Parallel Supercomputers
-
Dec.
-
Polychronopoulos CD and Kuck DJ. Guided Self-Scheduling: A Practical Scheduling Scheme for Parallel Supercomputers. Computers, IEEE Transactions on, C-36(12):1425-1439, Dec. 1987.
-
(1987)
Computers, IEEE Transactions on
, vol.C-36
, Issue.12
, pp. 1425-1439
-
-
Polychronopoulos, C.D.1
Kuck, D.J.2
-
25
-
-
80054884800
-
Exploiting parallelism on progressive alignment methods
-
Orobitg M, Guirado F, Notredame C, and Cores F. Exploiting parallelism on progressive alignment methods. The Journal of Supercomputing, pages 1-9, 2009.
-
(2009)
The Journal of Supercomputing
, pp. 1-9
-
-
Orobitg, M.1
Guirado, F.2
Notredame, C.3
Cores, F.4
-
26
-
-
77955093452
-
Parallelized pairwise sequence alignment using CUDA on multiple GPUs
-
Jung S. Parallelized pairwise sequence alignment using CUDA on multiple GPUs. BMC Bioinformatics, 10(Suppl 7):A3, 2009.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 7
-
-
Jung, S.1
-
27
-
-
74349123204
-
GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment
-
IEEE International Conference on High Performance Computing (HiPC 2006)
-
Liu W, Schmidt B, Voss G, and Müller-Wittig W. GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment. In IEEE International Conference on High Performance Computing (HiPC 2006), volume 4297 of Lecture Notes in Computer Science (LNCS), pages 363-374, 2006.
-
(2006)
Lecture Notes in Computer Science (LNCS)
, vol.4297
, pp. 363-374
-
-
Liu, W.1
Schmidt, B.2
Voss, G.3
Müller-Wittig, W.4
-
28
-
-
71049182306
-
MSA-CUDA: Multiple Sequence Alignment on graphics processing units with CUDA
-
July
-
Liu Y, Schmidt B, and Maskell DL. MSA-CUDA: Multiple Sequence Alignment on graphics processing units with CUDA. In Application-specific Systems, Architectures and Processors, 2009. ASAP 2009. 20th IEEE International Conference on, pages 121-128, July 2009.
-
(2009)
Application-specific Systems, Architectures and Processors, 2009. ASAP 2009. 20th IEEE International Conference on
, pp. 121-128
-
-
Liu, Y.1
Schmidt, B.2
Maskell, D.L.3
-
29
-
-
69949100622
-
Optimizing data intensive GPGPU computations for DNA sequence alignment
-
Trapnell C and Schatz MC. Optimizing data intensive GPGPU computations for DNA sequence alignment. Parallel Computing, 35(8-9):429-440, 2009.
-
(2009)
Parallel Computing
, vol.35
, Issue.8-9
, pp. 429-440
-
-
Trapnell, C.1
Schatz, M.C.2
-
30
-
-
44949272730
-
A time-efficient, linear-space local similarity algorithm
-
Huang X and Miller W. A time-efficient, linear-space local similarity algorithm. Advances in Applied Mathematics, 12:337-357, 1991.
-
(1991)
Advances in Applied Mathematics
, vol.12
, pp. 337-357
-
-
Huang, X.1
Miller, W.2
-
31
-
-
0025183708
-
Basic local alignment search tool
-
October
-
Altschul SF, Gish W, Miller W, Myers EW, and Lipman DJ. Basic local alignment search tool. Journal of molecular biology, 215(3):403-410, October 1990.
-
(1990)
Journal of Molecular Biology
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
32
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander C and Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Structure, Function, and Genetics, 9(1):56-68, 1991.
-
(1991)
Proteins: Structure, Function, and Genetics
, vol.9
, Issue.1
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
33
-
-
0032988850
-
BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
-
Thompson JD, Plewniak F, and Poch O. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics, 15(1):87-88, 1999.
-
(1999)
Bioinformatics
, vol.15
, Issue.1
, pp. 87-88
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
34
-
-
0031766401
-
HOMSTRAD: A database of protein structure alignments for homologous families
-
November
-
Mizuguchi K, Deane CM, Blundell TL, and Overington JP. HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci, 7(11):2469-2471, November 1998.
-
(1998)
Protein Sci
, vol.7
, Issue.11
, pp. 2469-2471
-
-
Mizuguchi, K.1
Deane, C.M.2
Blundell, T.L.3
Overington, J.P.4
-
35
-
-
0034855972
-
Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set
-
August
-
Karplus K and Hu B. Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set. Bioinformatics, 17(8):713-720, August 2001.
-
(2001)
Bioinformatics
, vol.17
, Issue.8
, pp. 713-720
-
-
Karplus, K.1
Hu, B.2
|