-
1
-
-
0035972742
-
Multiple alignment of complete sequences (MACS) in the postgenomic era
-
Lecompte,O., Thompson,J.D., Plewniak,F., Thierry,J. and Poch,O. (2001) Multiple alignment of complete sequences (MACS) in the postgenomic era. Gene, 270, 17-30.
-
(2001)
Gene
, vol.270
, pp. 17-30
-
-
Lecompte, O.1
Thompson, J.D.2
Plewniak, F.3
Thierry, J.4
Poch, O.5
-
2
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
Do,C.B., Mahabhashyam,M.S.P., Brudno,M. and Batzoglou,S. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
-
(2005)
Genome Res.
, vol.15
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.P.2
Brudno, M.3
Batzoglou, S.4
-
3
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
-i
-
Katoh,K., Kuma,K., -i., Toh,H. and Miyata,T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res., 33, 511-518.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
4
-
-
3042613056
-
Align-m - A new algorithm for multiple alignment of highly divergent sequences
-
Van Walle,I., Lasters,I. and Wyns,L. (2004) Align-m - a new algorithm for multiple alignment of highly divergent sequences. Bioinformatics, 20, 1428-1435.
-
(2004)
Bioinformatics
, vol.20
, pp. 1428-1435
-
-
Van Walle, I.1
Lasters, I.2
Wyns, L.3
-
5
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
6
-
-
17444401399
-
Evaluation of iterative alignment algorithms for multiple alignment
-
Wallace,I.M., O'Sullivan,O. and Higgins,D.G. (2005) Evaluation of iterative alignment algorithms for multiple alignment. Bioinformatics, 21, 1408-1414.
-
(2005)
Bioinformatics
, vol.21
, pp. 1408-1414
-
-
Wallace, I.M.1
O'Sullivan, O.2
Higgins, D.G.3
-
7
-
-
0036208872
-
Recent progress in multiple sequence alignment: A survey
-
Notredame,C. (2002) Recent progress in multiple sequence alignment: A survey. Pharmacogenomics, 3, 131-144.
-
(2002)
Pharmacogenomics
, vol.3
, pp. 131-144
-
-
Notredame, C.1
-
8
-
-
0025183708
-
Basic local alignment search tool
-
Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
9
-
-
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. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 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
-
10
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
-
(1988)
Proc. Natl Acad. Sci. USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
11
-
-
0025272240
-
Rapid and sensitive sequence comparison with FASTP and FASTA
-
Pearson,W.R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol., 183, 63-98.
-
(1990)
Methods Enzymol.
, vol.183
, pp. 63-98
-
-
Pearson, W.R.1
-
12
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
Lee,C., Grasso,C. and Sharlow,M.F. (2002) Multiple sequence alignment using partial order graphs. Bioinformatics, 18, 452-464.
-
(2002)
Bioinformatics
, vol.18
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
13
-
-
3543097981
-
Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
-
Grasso,C. and Lee,C. (2004) Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics, 20, 1546-1556.
-
(2004)
Bioinformatics
, vol.20
, pp. 1546-1556
-
-
Grasso, C.1
Lee, C.2
-
14
-
-
8744312854
-
A novel method for multiple alignment of sequences with repeated and shuffled elements
-
Raphael,B., Zhi,D., Tang,H. and Pevzner,P. (2004) A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res., 14, 2336-2346.
-
(2004)
Genome Res.
, vol.14
, pp. 2336-2346
-
-
Raphael, B.1
Zhi, D.2
Tang, H.3
Pevzner, P.4
-
15
-
-
0030582739
-
Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
-
Gotoh,O. (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol., 264, 823-838.
-
(1996)
J. Mol. Biol.
, vol.264
, pp. 823-838
-
-
Gotoh, O.1
-
16
-
-
0029046744
-
An assessment of amino acid exchange matrices in aligning protein sequences: The twilight zone revisited
-
Vogt,G., Etzold,T. and Argos,P. (1995) An assessment of amino acid exchange matrices in aligning protein sequences: The twilight zone revisited. J. Mol. Biol., 249, 816-831.
-
(1995)
J. Mol. Biol.
, vol.249
, pp. 816-831
-
-
Vogt, G.1
Etzold, T.2
Argos, P.3
-
17
-
-
0028047892
-
Sequence alignment and penalty choice. Review of concepts, case studies and implications
-
Vingron,M. and Waterman,M.S. (1994) Sequence alignment and penalty choice. Review of concepts, case studies and implications. J. Mol. Biol., 235, 1-12.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1-12
-
-
Vingron, M.1
Waterman, M.S.2
-
18
-
-
0030934592
-
Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of apicomplexa
-
Morrison,D.A. and Ellis,J.T. (1997) Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of apicomplexa. Mol. Biol. Evol., 14, 428-441.
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 428-441
-
-
Morrison, D.A.1
Ellis, J.T.2
-
19
-
-
0034043777
-
The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence
-
Hickson,R.E., Simon,C. and Perrey,S.W. (2000) The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Mol. Biol. Evol., 17, 530-539.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 530-539
-
-
Hickson, R.E.1
Simon, C.2
Perrey, S.W.3
-
20
-
-
0003516147
-
-
Cambridge University Press
-
Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) In Biological Sequence Analysis. Cambridge University Press, pp. 134-159.
-
(1998)
Biological Sequence Analysis
, pp. 134-159
-
-
Durbin, R.1
Eddy, S.2
Krogh, A.3
Mitchison, G.4
-
21
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
Thompson,J.D., Plewniak,F. and Poch,O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
22
-
-
0037010180
-
Quality assessment of multiple alignment programs
-
Lassmann,T. and Sonnhammer,E.L.L. (2002) Quality assessment of multiple alignment programs. FEBS Lett., 529, 126-130.
-
(2002)
FEBS Lett.
, vol.529
, pp. 126-130
-
-
Lassmann, T.1
Sonnhammer, E.L.L.2
-
23
-
-
0037433035
-
AltAVisT: Comparing alternative multiple sequence alignments
-
Morgenstern,B., Goel,S., Sczyrba,A. and Dress,A. (2003) AltAVisT: comparing alternative multiple sequence alignments. Bioinformatics, 19, 425-426.
-
(2003)
Bioinformatics
, vol.19
, pp. 425-426
-
-
Morgenstern, B.1
Goel, S.2
Sczyrba, A.3
Dress, A.4
-
24
-
-
0029861894
-
Multiple DNA and protein sequence alignment based on segment-to-segment comparison
-
Morgenstern,B., Dress,A. and Werner,T. (1996) Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl Acad. Sci. USA, 93, 12098-12103.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 12098-12103
-
-
Morgenstern, B.1
Dress, A.2
Werner, T.3
-
25
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
26
-
-
0032945593
-
DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
-
Morgenstern,B. (1999) DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15, 211-218.
-
(1999)
Bioinformatics
, vol.15
, pp. 211-218
-
-
Morgenstern, B.1
-
27
-
-
0033006303
-
Combining many multiple alignments in one improved alignment
-
Bucka-Lassen,K., Caprani,O. and Hein,J. (1999) Combining many multiple alignments in one improved alignment. Bioinformatics, 15, 122-130.
-
(1999)
Bioinformatics
, vol.15
, pp. 122-130
-
-
Bucka-Lassen, K.1
Caprani, O.2
Hein, J.3
-
28
-
-
0043123123
-
Tcoffeeιgs: A web server for computing, evaluating and combining multiple sequence alignments
-
Poirot,O., O'Toole,E. and Notredame,C. (2003) Tcoffeeιgs: A web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res., 31, 3503-3506.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3503-3506
-
-
Poirot, O.1
O'Toole, E.2
Notredame, C.3
-
29
-
-
3042661708
-
APDB: A novel measure for benchmarking sequence alignment methods without reference alignments
-
O'Sullivan,O., Zehnder,M., Higgins,D., Bucher P., Grosdidier,A. and Notredame,C. (2003) APDB: A novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics, 19 (Supp). 1), 215-221.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
, pp. 215-221
-
-
O'Sullivan, O.1
Zehnder, M.2
Higgins, D.3
Bucher, P.4
Grosdidier, A.5
Notredame, C.6
-
30
-
-
31144458620
-
-
R Development Core Team R: A Language and Environment for Statistical Computing R Foundation for Statistical Computing Vienna, Austria ISBN 3-900051-07-0
-
R Development Core Team R: A Language and Environment for Statistical Computing R Foundation for Statistical Computing Vienna, Austria (2005), ISBN 3-900051-07-0.
-
(2005)
-
-
-
31
-
-
0032988850
-
BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
-
Thompson,J.D., Plewniak,F. and Poch,O. (1999) BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics, 15, 87-88.
-
(1999)
Bioinformatics
, vol.15
, pp. 87-88
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
32
-
-
24644457706
-
BaliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
-
Thompson,J.D., Koehl,P., Ripp,R. and Poch,O. (2005) BaliBASE 3.0: Latest developments of the multiple sequence alignment benchmark. Proteins, 61, 127-136.
-
(2005)
Proteins
, vol.61
, pp. 127-136
-
-
Thompson, J.D.1
Koehl, P.2
Ripp, R.3
Poch, O.4
-
33
-
-
16344394781
-
SABmark - A benchmark for sequence alignment that covers the entire known fold space
-
Van Walle,I., Lasters,I. and Wyns,L. (2005) SABmark - a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics, 21, 1267-1268.
-
(2005)
Bioinformatics
, vol.21
, pp. 1267-1268
-
-
Van Walle, I.1
Lasters, I.2
Wyns, L.3
-
34
-
-
0035824873
-
Towards a reliable objective function for multiple sequence alignments
-
Thompson,J.D., Plewniak,F., Ripp,R., Thierry,J.C. and Poch,O. (2001) Towards a reliable objective function for multiple sequence alignments. J. Mol. Biol., 314, 937-951.
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 937-951
-
-
Thompson, J.D.1
Plewniak, F.2
Ripp, R.3
Thierry, J.C.4
Poch, O.5
-
35
-
-
0034843597
-
AL2CO: Calculation of positional conservation in a protein sequence alignment
-
Pei,J. and Grishin,N.V. (2001) AL2CO: Calculation of positional conservation in a protein sequence alignment. Bioinformatics, 17. 700-712.
-
(2001)
Bioinformatics
, vol.17
, pp. 700-712
-
-
Pei, J.1
Grishin, N.V.2
-
36
-
-
0036737479
-
The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs
-
Griffiths-Jones,S. and Bateman,A. (2002) The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs. Bioinformatics, 18, 1243-1249.
-
(2002)
Bioinformatics
, vol.18
, pp. 1243-1249
-
-
Griffiths-Jones, S.1
Bateman, A.2
-
37
-
-
0027968068
-
CLUSTALW: 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. (1994) CLUSTALW: 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.D.1
Higgins, D.G.2
Gibson, T.J.3
-
38
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh,K., Misawa,K., Kuma,K.-i. and Miyata T. (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
Misawa, K.2
Kuma, K.-I.3
Miyata, T.4
|