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Bibliography

1
L. Allison and C.S. Wallace.
The posterior probability distribution of alignments and its application to parameter estimation of evolutionary trees and to optimization of multiple alignments.
J. Molecular Evolution, 39:418-430, 1994.

2
Lachlan H. Bell, John R. Coggins, and James E. Milner-White.
Mix'n'match: an improved multiple sequence alignment procedure for distantly related proteins using secondary structure predictions, designed to be independent of the choice of gap penalty and scoring matrix.
Protein Engineering, 6(7):683-690, 1993.

3
Steven A. Benner, Mark A. Cohen, and Gaston H. Gonnet.
Empirical and structural models for insertions and deletions in the divergent evolution of proteins.
J. Molecular Biology, 229:1065-1082, 1993.

4
Steven A. Benner, Mark A. Cohen, and Gaston H. Gonnet.
Amino acid substitution during functionally constrained divergent evolution of protein sequences.
Protein Engineering, 7(11), 1994.

5
Humberto Carillo and David. Lipman.
The multiple sequence alignment problem in biology.
SIAM J. Appl. Math., 48(5):1073-1082, 1988.

6
Margaret O. Dayhoff, R. M. Schwartz, and B. C. Orcutt.
A model for evolutionary change in proteins.
In Margaret O. Dayhoff, editor, Atlas of Protein Sequence and Structure, volume 5, pages 345-352. National Biochemical Research Foundation, Washington DC, 1978.

7
Adam Godzik and Jeffrey Skolnick.
Flexible algorithm for direct multiple alignment of protein structures and sequences.
CABIOS, 10(6):587-596, 1994.

8
Gaston H. Gonnet, Mark A. Cohen, and Steven A. Benner.
Exhaustive matching of the entire protein sequence database.
Science, 256:1443-1445, 1992.

9
Gaston H. Gonnet and Chantal Korostensky.
Evaluation measures of multiple sequence alignments.
In preparation, 1996.

10
O. Gotoh.
An improved algorithm for matching biological sequences.
J. Mol. Biol., 162:705-708, 1982.

11
Sandeep K. Gupta, John Kececioglu, and Alejandro A. Schaffer.
Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment.
J. Computational Biology, 1996.
To appear.

12
Xiaoqiu Huang.
On global sequence alignment.
CABIOS, 10(3):227-235, 1994.

13
Charles E. Lawrence, Stephen F. Altschul, Mark S. Boguski, Jun S. Liu, Andrew F. Neuwald, and John C. Wootton.
Detecting subtle sequence signals: A gibbs sampling strategy for multiple alignment.
Science, 262:208-214, October 1993.

14
David J. Lipman, Stephen F. Altschul, and John D. Kececioglu.
A tool for multiple sequence alignment.
Proc. Natl. Acad. Sci. USA, 86:4412-4415, June 1989.

15
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.

16
Gregory D. Schuler, Stephen F. Altschul, and David J. Lipman.
A workbench for multiple alignment construction and analysis.
PROTEINS: Structure, Function, and Genetics, 9:180-190, 1991.

17
Peter H. Sellers.
On the theory and computation of evolutionary distances.
SIAM J Appl. Math., 26(4):787-793, Jun 1974.

18
Temple F. Smith and Michael S. Waterman.
Identification of common molecular subsequences.
J. Mol. Biol., 147:195-197, 1981.

19
J.D. Thompson, D.G. Higgins, and T.J 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.



Gaston Gonnet
1998-07-14