-
1
-
-
0022899010
-
Optimal sequence alignment using affine gap costs
-
S. Altschul and B. W. Erickson. Optimal sequence alignment using affine gap costs. J. Mol. Biol., 48:603-1 6, 1986.
-
(1986)
J. Mol. Biol.
, vol.48
, pp. 603-616
-
-
Altschul, S.1
Erickson, B.W.2
-
3
-
-
0028011075
-
Hidden markov models of biological primary sequence information
-
P. Baldi, Y. Chauvin, T. Hunkapiller, and M. A. McClure. Hidden markov models of biological primary sequence information. Proc. Natl. Acad. Sci. USA, 91:1059-1063, 1994.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 1059-1063
-
-
Baldi, P.1
Chauvin, Y.2
Hunkapiller, T.3
McClure, M.A.4
-
4
-
-
0027483434
-
Empirical and structural models for insertions and deletions in the divergent evolution of proteins
-
S. A. Benner, M. A. Cohen, and G. H. Gonnet. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J. Molecular Biology, 229:1065-1082, 1993.
-
(1993)
J. Molecular Biology
, vol.229
, pp. 1065-1082
-
-
Benner, S.A.1
Cohen, M.A.2
Gonnet, G.H.3
-
5
-
-
0000303438
-
The multiple sequence alignment problem in biology
-
H. Carillo and D. Lipman. The multiple sequence alignment problem in biology. SIAM J. Appl. Math., 48(5):1073-1082, 1988.
-
(1988)
SIAM J. Appl. Math.
, vol.48
, Issue.5
, pp. 1073-1082
-
-
Carillo, H.1
Lipman, D.2
-
6
-
-
0000228203
-
A model for evolutionary change in proteins
-
In M. O. Dayhoff, editor
-
M. O. Dayhoff, R. M. Schwartz, and B. C. Orcutt. A model for evolutionary change in proteins. In M. O. Dayhoff, editor, Atlas of Protein Sequence and Structure, volume 5, pages 345-352. 1978.
-
(1978)
Atlas of Protein Sequence and Structure
, vol.5
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
7
-
-
0023084055
-
Progressive sequence alignment as a prerequisite to correct phylogenetic trees
-
D. Feng and R. F. Doolittle. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25:351-60, 1987.
-
(1987)
J. Mol. Evol.
, vol.25
, pp. 351-360
-
-
Feng, D.1
Doolittle, R.F.2
-
8
-
-
0003081588
-
The steiner problem in phylogeny is np-complete
-
L. R. Foulds and R. L. Graham. The steiner problem in phylogeny is np-complete. Proc. Natl. Academy Science, 3:43-49, 1982.
-
(1982)
Proc. Natl. Academy Science
, vol.3
, pp. 43-49
-
-
Foulds, L.R.1
Graham, R.L.2
-
10
-
-
0026656815
-
Exhaustive matching of the entire protein sequence database
-
G. H. Gonnet, M. A. Cohen, and S. A. Benner. Exhaustive matching of the entire protein sequence database. Science, 256:1443-1445, 1992.
-
(1992)
Science
, vol.256
, pp. 1443-1445
-
-
Gonnet, G.H.1
Cohen, M.A.2
Benner, S.A.3
-
11
-
-
0007434761
-
Evaluation measures of multiple sequence alignments
-
submitted
-
G. H. Gonnet and C. Korostensky. Evaluation measures of multiple sequence alignments. J. Comp. Biol., 1999. submitted.
-
(1999)
J. Comp. Biol.
-
-
Gonnet, G.H.1
Korostensky, C.2
-
12
-
-
0020484488
-
An improved algorithm for matching biological sequences
-
O. Gotoh. An improved algorithm for matching biological sequences. J. Mol. Biol., 162:705-708, 1982.
-
(1982)
J. Mol. Biol.
, vol.162
, pp. 705-708
-
-
Gotoh, O.1
-
13
-
-
0026220441
-
Solution of large-scale symmetric traveling salesmand problems
-
M. Groetschel and O. Holland. Solution of large-scale symmetric traveling salesmand problems. Math. Programming, pages 141-202, 1991.
-
(1991)
Math. Programming
, pp. 141-202
-
-
Groetschel, M.1
Holland, O.2
-
14
-
-
3643075904
-
Making the shortest-paths approach to sum-of-pairs multiple sequence alignment more space efficient in practice
-
S. Gupta, J. Kececioglu, and A. Schaffer. Making the shortest-paths approach to sum-of-pairs multiple sequence alignment more space efficient in practice. Proc. 6th Symp. on Combinatorial Pattern Matching, pages 128-43, 1995.
-
(1995)
Proc. 6th Symp. On Combinatorial Pattern Matching
, pp. 128-143
-
-
Gupta, S.1
Kececioglu, J.2
Schaffer, A.3
-
15
-
-
0003290663
-
Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment
-
S. K. Gupta, J. Kececioglu, and A. A. Schaffer. Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. In J. Computational Biology, 1996.
-
(1996)
J. Computational Biology
-
-
Gupta, S.K.1
Kececioglu, J.2
Schaffer, A.A.3
-
16
-
-
0027351056
-
Efficient methods for multiple sequence alignment with guaranteed error bounds
-
D. Gusfield. Efficient methods for multiple sequence alignment with guaranteed error bounds. Bull. Math. Biol., 55:141-54, 1993.
-
(1993)
Bull. Math. Biol.
, vol.55
, pp. 141-154
-
-
Gusfield, D.1
-
17
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
S. Henikoff and J. G. Henikoff. Amino acid substitution matrices from protein blocks. Proc. Natl. Academy Science, 89:10915-19, 1992.
-
(1992)
Proc. Natl. Academy Science
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
18
-
-
0030013081
-
Blocks database and its applicatioins
-
In R. F. Doolittle, editor Academic Press, New York
-
S. Henikoff and J. G. Henikoff. Blocks database and its applicatioins. In R. F. Doolittle, editor, Methods in Enzymology, volume 266 of Computer methods for macromolecular sequence analysis, pages 88-105. Academic Press, New York, 1996.
-
(1996)
Methods in Enzymology of Computer Methods for Macromolecular Sequence Analysis
, vol.266
, pp. 88-105
-
-
Henikoff, S.1
Henikoff, J.G.2
-
19
-
-
0028928174
-
Comprehensive study on iterative algorithms of multiple sequence alignment
-
M. Hirosawa, Y. Totoki, M. Hoshida, and M. Ishikawa. Comprehensive study on iterative algorithms of multiple sequence alignment. CABIOS, 11(1):13-18, 1995.
-
(1995)
CABIOS
, vol.11
, Issue.1
, pp. 13-18
-
-
Hirosawa, M.1
Totoki, Y.2
Hoshida, M.3
Ishikawa, M.4
-
20
-
-
0028679709
-
On the complexity of multiple sequence alignment
-
T. Jiang and L. Wang. On the complexity of multiple sequence alignment. J. Comp. Biol., 1:337-48, 1994.
-
(1994)
J. Comp. Biol.
, vol.1
, pp. 337-348
-
-
Jiang, T.1
Wang, L.2
-
21
-
-
0000880429
-
Approximation algorithms for tree alignment with a given phylogeny
-
T. Jiang, L. Wang, and E. L. Lawler. Approximation algorithms for tree alignment with a given phylogeny. Algorithmica, 16:302-15, 1996.
-
(1996)
Algorithmica
, vol.16
, pp. 302-315
-
-
Jiang, T.1
Wang, L.2
Lawler, E.L.3
-
22
-
-
0000689820
-
More approaches to the travelling salesman guide
-
December
-
D. Johnson. More approaches to the travelling salesman guide. Nature, 330:525, December 1987.
-
(1987)
Nature
, vol.330
, pp. 525
-
-
Johnson, D.1
-
23
-
-
85031901109
-
Local optimization and the traveling salesman problem
-
In Proc. 17th Colloq. on Automata, Languages and Programming Berlin Springer Verlag
-
D. Johnson. Local optimization and the traveling salesman problem. In Proc. 17th Colloq. on Automata, Languages and Programming, volume 443 of Lecture Notes in Computer Science, pages 446-461, Berlin, 1990. Springer Verlag.
-
(1990)
Lecture Notes in Computer Science
, vol.443
, pp. 446-461
-
-
Johnson, D.1
-
25
-
-
0028181441
-
Hidden markov models in computational biology: Applications to protein modeling
-
A. Krogh, M. Brown, I. S.Mian, K. Sjolander, and D. Haussler. Hidden markov models in computational biology: Applications to protein modeling. J. Molecular Biology, 235:1501-1531, 1994.
-
(1994)
J. Molecular Biology
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.S.3
Sjolander, K.4
Haussler, D.5
-
26
-
-
0024284078
-
A flexible multiple sequence alignment program
-
H. Martinez. A flexible multiple sequence alignment program. Nucleic Acids Res., 16:1683-1691, 1988.
-
(1988)
Nucleic Acids Res.
, vol.16
, pp. 1683-1691
-
-
Martinez, H.1
-
27
-
-
0028341506
-
Comparative analysis of mutliple protein sequence alignment methods
-
M. McClure, T. Vasi, and W. Fitch. Comparative analysis of mutliple protein sequence alignment methods. J. Mol. Biol. Evol, 11(4):571-592, 1994.
-
(1994)
J. Mol. Biol. Evol
, vol.11
, Issue.4
, pp. 571-592
-
-
McClure, M.1
Vasi, T.2
Fitch, W.3
-
28
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
S. B. Needleman and C. D. Wunsch. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48:443-453, 1970.
-
(1970)
J. Mol. Biol.
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
29
-
-
0026124209
-
A branch-and-cut algorithm for the resolution of large-scale symmetric traveling salesman problems
-
M. Padberg and G. Rinaldi. A branch-and-cut algorithm for the resolution of large-scale symmetric traveling salesman problems. SIAM Review, 33:60-100, 1991.
-
(1991)
SIAM Review
, vol.33
, pp. 60-100
-
-
Padberg, M.1
Rinaldi, G.2
-
30
-
-
0013695811
-
Approximation algorithms for multiple sequence alignments under a fixed evolutionary tree
-
R. Roui and J. Kececioglu. Approximation algorithms for multiple sequence alignments under a fixed evolutionary tree. Discrete Applied Mathematics, pages 355-366, 1998.
-
(1998)
Discrete Applied Mathematics
, pp. 355-366
-
-
Roui, R.1
Kececioglu, J.2
-
31
-
-
0001213953
-
Simultaneous comparison of tree or more sequences related by a tree
-
In D. Sankoff and G. Kruskal, editors Addison Wesley, Reading MA
-
D. Sankoff and R. Cedergren. Simultaneous comparison of tree or more sequences related by a tree. In D. Sankoff and G. Kruskal, editors, Time Warps, String Edits, and Marcomolecules: The Theory and Practice of Seqeunce Comparison, volume 28, pages 253-263. Addison Wesley, Reading MA, 1983.
-
(1983)
Time Warps, String Edits, and Marcomolecules: The Theory and Practice of Seqeunce Comparison
, vol.28
, pp. 253-263
-
-
Sankoff, D.1
Cedergren, R.2
-
32
-
-
0019887799
-
Identification of common molecular subsequences
-
T. F. Smith and M. S. Waterman. Identification of common molecular subsequences. J. Mol. Biol., 147:195-197, 1981.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
33
-
-
0023364009
-
Multiple sequence alignment by a pairwise algorithm
-
W. Taylor. Multiple sequence alignment by a pairwise algorithm. Comput. Appl. Biosci., 3:81-87, 1987.
-
(1987)
Comput. Appl. Biosci.
, vol.3
, pp. 81-87
-
-
Taylor, W.1
-
34
-
-
0024245156
-
A flexible method to align a large number of sequences
-
W. Taylor. A flexible method to align a large number of sequences. J. Mol. Evol., 28:161-169, 1988.
-
(1988)
J. Mol. Evol.
, vol.28
, pp. 161-169
-
-
Taylor, W.1
-
35
-
-
0027968068
-
Clustal w: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
-
J. Thompson, D. Higgins, and T. Gibson. Clustal w: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22:4673-4680, 1994.
-
(1994)
Nucleic Acids Research
, vol.22
, pp. 4673-4680
-
-
Thompson, J.1
Higgins, D.2
Gibson, T.3
-
37
-
-
0000220975
-
Line geometries for sequence comparison
-
M. Waterman and M. Perlwitz. Line geometries for sequence comparison. Bull. Math. Biol., 46:567-577, 1984.
-
(1984)
Bull. Math. Biol.
, vol.46
, pp. 567-577
-
-
Waterman, M.1
Perlwitz, M.2
-
38
-
-
0027570680
-
A multiple sequence comparison method
-
A. Wong, S. Chan, and D. Chiu. A multiple sequence comparison method. Society for Mathematical Biology, 55(2):465-486, 1993.
-
(1993)
Society for Mathematical Biology
, vol.55
, Issue.2
, pp. 465-486
-
-
Wong, A.1
Chan, S.2
Chiu, D.3
|