-
1
-
-
34548348538
-
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization
-
Bauer, M. et al. (2007) Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics, 8, 271.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 271
-
-
Bauer, M.1
-
2
-
-
0001096735
-
Genetic algorithms and random keys for sequencing and optimization
-
Bean, J.C. (1994) Genetic algorithms and random keys for sequencing and optimization. ORSA J. Comput., 6, 154-160.
-
(1994)
ORSA J. Comput.
, vol.6
, pp. 154-160
-
-
Bean, J.C.1
-
3
-
-
58249121729
-
RNAalifold: improved consensus structure prediction for RNA alignments
-
Bernhart, S. et al. (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9, 474.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 474
-
-
Bernhart, S.1
-
4
-
-
33745612985
-
STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time
-
Dalli, D. et al. (2006) STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time. Bioinformatics, 22, 1593-1599.
-
(2006)
Bioinformatics
, vol.22
, pp. 1593-1599
-
-
Dalli, D.1
-
6
-
-
0036530772
-
A fast elitist multi-objective genetic algorithm: NSGA-II
-
Deb, K. et al. (2000) A fast elitist multi-objective genetic algorithm: NSGA-II. IEEE Trans. Evol. Comput., 6, 182-197.
-
(2000)
IEEE Trans. Evol. Comput.
, vol.6
, pp. 182-197
-
-
Deb, K.1
-
7
-
-
3042554001
-
An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots
-
Dirks, R.M. and Pierce, N.A. (2004) An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. J. Comput. Chem., 25, 1295-1304.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1295-1304
-
-
Dirks, R.M.1
Pierce, N.A.2
-
8
-
-
46249114849
-
A max-margin model for efficient simultaneous alignment and folding of RNA sequences
-
Do, C.B. et al. (2008) A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics, 24, 68-76.
-
(2008)
Bioinformatics
, vol.24
, pp. 68-76
-
-
Do, C.B.1
-
9
-
-
33749412683
-
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
-
Dowell, R. and Eddy, S. (2006) Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics, 7, 400.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 400
-
-
Dowell, R.1
Eddy, S.2
-
10
-
-
58149191274
-
Rfam: updates to the RNA families database
-
Gardner, P.P. et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37, D136-D140.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Gardner, P.P.1
-
12
-
-
0035873307
-
Discovering common stem-loop motifs in unaligned RNA sequences
-
Gorodkin, J. et al. (2001) Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res., 29, 2135-2144.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2135-2144
-
-
Gorodkin, J.1
-
13
-
-
75849160582
-
CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score
-
Hamada, M. et al. (2009) CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinformatics, 25, 3236-3243.
-
(2009)
Bioinformatics
, vol.25
, pp. 3236-3243
-
-
Hamada, M.1
-
14
-
-
34248385237
-
Multiobjective optimization in bioinformatics and computational biology
-
Handl, J. et al. (2007) Multiobjective optimization in bioinformatics and computational biology. IEEE/ACM Trans. Comput. Biol. Bioinform., 4, 279-292.
-
(2007)
IEEE/ACM Trans. Comput. Biol. Bioinform.
, vol.4
, pp. 279-292
-
-
Handl, J.1
-
15
-
-
34248632816
-
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign
-
Harmanci, A. et al. (2007) Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinformatics, 8, 130.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 130
-
-
Harmanci, A.1
-
16
-
-
42449109109
-
PARTS: probabilistic alignment for RNA joint secondary structure prediction
-
Harmanci, A. et al. (2008) PARTS: probabilistic alignment for RNA joint secondary structure prediction. Nucleic Acids Res., 36, 2406-2417.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 2406-2417
-
-
Harmanci, A.1
-
17
-
-
35748971022
-
Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix
-
Havgaard, J. et al. (2007) Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput. Biol., 3, 1896-1908.
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. 1896-1908
-
-
Havgaard, J.1
-
18
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker, I. et al. (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem., 125, 167-188.
-
(1994)
Monatsh. Chem.
, vol.125
, pp. 167-188
-
-
Hofacker, I.1
-
19
-
-
25444433586
-
Accelerated probabilistic inference of RNA structure evolution
-
Holmes, I. (2005) Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics, 6, 73.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 73
-
-
Holmes, I.1
-
20
-
-
0142165034
-
Reducing the run-time complexity of multiobjective EAs: the NSGA-II and other algorithms
-
Jensen, M.T. (2003) Reducing the run-time complexity of multiobjective EAs: the NSGA-II and other algorithms. IEEE Trans. Evol. Comput., 7, 503-515.
-
(2003)
IEEE Trans. Evol. Comput.
, vol.7
, pp. 503-515
-
-
Jensen, M.T.1
-
21
-
-
0037100671
-
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh, K. et al. (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
-
22
-
-
33847262911
-
Robust prediction of consensus secondary structures using averaged base pairing probability matrices
-
Kiryu, H. et al. (2007a) Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinformatics, 23, 434-441.
-
(2007)
Bioinformatics
, vol.23
, pp. 434-441
-
-
Kiryu, H.1
-
23
-
-
34547844102
-
Murlet: a practical multiple alignment tool for structural RNA sequences
-
Kiryu, H. et al. (2007b) Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics, 23, 1588-1598.
-
(2007)
Bioinformatics
, vol.23
, pp. 1588-1598
-
-
Kiryu, H.1
-
24
-
-
2942544566
-
RSEARCH: finding homologs of single structured RNA sequences
-
Klein, R. and Eddy, S. (2003) RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics, 4, 44.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 44
-
-
Klein, R.1
Eddy, S.2
-
25
-
-
36949011603
-
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing
-
Lindgreen, S. et al. (2007) MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics, 23, 3304-3311.
-
(2007)
Bioinformatics
, vol.23
, pp. 3304-3311
-
-
Lindgreen, S.1
-
26
-
-
19544374354
-
Predicting a set of minimal free energy RNA secondary structures common to two sequences
-
Mathews, D. (2005) Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics, 21, 2246-2253.
-
(2005)
Bioinformatics
, vol.21
, pp. 2246-2253
-
-
Mathews, D.1
-
27
-
-
34548443728
-
SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework
-
Meyer, I.M. and Miklos, I. (2007) SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Comput. Biol., 3, e149.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Meyer, I.M.1
Miklos, I.2
-
28
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman, S. and Wunsch, C. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
-
(1970)
J. Mol. Biol.
, vol.48
, pp. 443-453
-
-
Needleman, S.1
Wunsch, C.2
-
29
-
-
0029872694
-
SAGA: sequence alignment by genetic algorithm
-
Notredame, C. and Higgins, D. (1996) SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res., 24, 1515-1524.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 1515-1524
-
-
Notredame, C.1
Higgins, D.2
-
30
-
-
0030813152
-
RAGA: RNA sequence alignment by genetic algorithm
-
Notredame, C. et al. (1997) RAGA: RNA sequence alignment by genetic algorithm. Nucleic Acids Res., 25, 4570-4580.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 4570-4580
-
-
Notredame, C.1
-
31
-
-
68349160992
-
Experiments with Bicriteria Sequence Alignment
-
Shi, Y. et al. (eds) Springer, Berlin Heidelberg
-
Paquete, L. and Almeida, J.P.O. (2009) Experiments with Bicriteria Sequence Alignment. In Shi, Y. et al. (eds) Cutting-Edge Research Topics on Multiple Criteria Decision Making, volume 35 of Communications in Computer and Information Science. Springer, Berlin Heidelberg, pp. 45-51 .
-
(2009)
Cutting-Edge Research Topics on Multiple Criteria Decision Making, volume 35 of Communications in Computer and Information Science
, pp. 45-51
-
-
Paquete, L.1
Almeida, J.P.O.2
-
32
-
-
24144497144
-
Consensus shapes: an alternative to the Sankoff algorithm for RNAconsensus structure prediction
-
Reeder, J. and Giegerich, R. (2005) Consensus shapes: an alternative to the Sankoff algorithm for RNAconsensus structure prediction. Bioinformatics, 21, 3516-3523.
-
(2005)
Bioinformatics
, vol.21
, pp. 3516-3523
-
-
Reeder, J.1
Giegerich, R.2
-
33
-
-
0033162059
-
Pareto-optimal alignment of biological sequences
-
Roytberg, M.A. et al. (1999) Pareto-optimal alignment of biological sequences. Biophysics, 44, 565-577.
-
(1999)
Biophysics
, vol.44
, pp. 565-577
-
-
Roytberg, M.A.1
-
34
-
-
0022146059
-
Simultaneous solution of the RNA folding, alignment and protosequence problems
-
Sankoff, D. (1985) Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math., 45, 810-825.
-
(1985)
SIAM J. Appl. Math.
, vol.45
, pp. 810-825
-
-
Sankoff, D.1
-
35
-
-
15444361843
-
Acommon core of secondary structure of the internal transcribed spacer 2 (its2) throughout the eukaryota
-
Schultz, J. et al. (2005)Acommon core of secondary structure of the internal transcribed spacer 2 (its2) throughout the eukaryota. RNA, 11, 361-364.
-
(2005)
RNA
, vol.11
, pp. 361-364
-
-
Schultz, J.1
-
36
-
-
38549087890
-
The ITS2 Database II: homology modelling RNA structure for molecular systematics
-
Selig, C. et al. (2008) The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Res., 36, D377-D380.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Selig, C.1
-
37
-
-
58949101491
-
An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast
-
Taneda, A. (2008) An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast. BMC Bioinformatics, 9, 521.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 521
-
-
Taneda, A.1
-
38
-
-
0027968068
-
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J. et al. (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
-
-
Thompson, J.1
-
39
-
-
0032988850
-
BAliBASE: a benchmark alignments database for the evaluation of multiple sequence alignment programs
-
Thompson, J. et al. (1999) BAliBASE: a benchmark alignments database for the evaluation of multiple sequence alignment programs. Bioinformatics, 15, 87-88.
-
(1999)
Bioinformatics
, vol.15
, pp. 87-88
-
-
Thompson, J.1
-
40
-
-
34247598415
-
Inferring noncoding RNAfamilies and classes by means of genome-scale structure-based clustering
-
Will, S. et al. (2007) Inferring noncoding RNAfamilies and classes by means of genome-scale structure-based clustering. PLoS Comp. Biol., 3, e65.
-
(2007)
PLoS Comp. Biol.
, vol.3
-
-
Will, S.1
-
41
-
-
34248374330
-
An enhanced RNA alignment benchmark for sequence alignment programs
-
Wilm, A. et al. (2006) An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol. Biol., 1, 19.
-
(2006)
Algorithms Mol. Biol.
, vol.1
, pp. 19
-
-
Wilm, A.1
-
42
-
-
34548131258
-
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
-
Xu, X. et al. (2007) RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics, 23, 1883-1891.
-
(2007)
Bioinformatics
, vol.23
, pp. 1883-1891
-
-
Xu, X.1
|