DCA: Divide-and-Conquer Multiple Sequence Alignment - References

A Divide and Conquer Approach to Multiple Alignment
A.W.M. Dress, G.Füllen, S.W. Perrey
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB 95), AAAI Press, Menlo Park, CA, USA, 107-113, 1995.

A General Method for Fast Multiple Sequence Alignment
U. Tönges, S.W. Perrey, J. Stoye, A.W.M. Dress
Gene 172(1), GC33-GC41, 1996. (Gene-COMBIS)

Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment
S.W. Perrey, J. Stoye
Information and Mathematical Sciences Reports, Series B:96/06 (ISSN 1171-7637), May 1996

Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment
J.Stoye, S.W. Perrey, A.W.M. Dress
Appl. Math. Lett. 10(2), 67-73, 1997.

Divide-and-Conquer Multiple Sequence Alignment
J. Stoye
Dissertation Thesis. Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik, Report 97-02, 1997. (ISSN 0946-7831)

Two Applications of the Divide & Conquer Principle in the Molecular Sciences
G. Brinkmann, A.W.M. Dress, S.W. Perrey, J. Stoye
Mathematical Programming 79, 71-97, 1997.

DCA: An Efficient Implementation of the Divide-and-Conquer Multiple Sequence Alignment Algorithm
>J. Stoye, V. Moulton, A.W.M. Dress
CABIOS 13(6), 625-626, 1997.

On Simultaneous versus Iterative Multiple Sequence Alignment
S.W. Perrey, J. Stoye, V. Moulton, A.W.M. Dress
Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse. Materialien/Preprints 111, 1997.

FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment
S.W. Perrey, J. Stoye, V. Moulton
Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse. Materialien/Preprints 114, 1997.

Multiple Sequence Alignment with the Divide-and-Conquer Method
J. Stoye
Gene 211(2), GC45-GC56, 1998. (Gene-COMBIS)

Further References

Trees, Stars, and Multiple Biological Sequence Alignments
S.F. Altschul, D.J. Lipman
SIAM J. Appl. Math. 49(1), 197-209, 1989.

The Multiple Sequence Alignment Problem in Biology
H. Carrillo, D.J. Lipman
SIAM J. Appl. Math. 48(5), 1073-1082, 1988.

Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences
R.F. Doolittle, editor
Vol. 183 of Methods in Enzymology Academic Press, Inc., San Diego, CA, USA, 1990.

Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment
S.K. Gupta, J.D. Kececioglu, A.A. Schäffer
J. Comp. Biol. 2(3), 459-472, 1995.

A Dictionary of Protein Secondary Structure
W. Kabsch and C. Sander
Biopolymers 22, 2577-2637, 1983.

The Maximum Weight Trace Problem in Multiple Sequence Alignment
J. Kececioglu
In A. Apostolico, M. Crochemore, Z. Galil, and U. Manber, editors, 4th Annual Symposium, CPM 93, Padova, Italy, June 2-4, 1993. Proceedings, number 684 in Lecture Notes in Computer Science, pages 106-119, Berlin, 1993. Springer Verlag.

The Order of Sequence Alignment Can Bias the Selection of Tree Topology
J.A. Lake
Mol. Biol. Evol. 8(3), 378-385, 1991.

A Tool for Multiple Sequence Alignment
D.J. Lipman, S.F. Altschul, J. Kececioglu
Proc. Natl. Acad. Sci. USA, 86, 4412-4415, 1989.

Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment
B. Morgenstern, J. Stoye, A.W.M. Dress
Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse. Materialien/Preprints 133, 1999.

Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison
D. Sankoff, J.B. Kruskal, editors
Addison-Wesley, Reading, MA, USA, 1983.

Freeing Phylogenies from Artifacts of Alignment
J.L. Thorne, H. Kishino
Mol. Biol. Evol. 9(6), 1148-1162, 1992.

Motif Recognition and Alignment for Many Sequences by Comparison of Dot-matrices
M. Vingron, P. Argos
J. Mol. Biol. 218, 33-43, 1991.

On the Complexity of Multiple Sequence Alignment
L. Wang, T. Jiang
J. Comp. Biol. 1(4), 337-348, 1994.

Sequence Alignments in the Neighborhood of the Optimum with General Application to Dynamic Programming
M.S. Waterman
Proc. Natl. Acad. Sci. USA 80, 3132-3124, 1983.

Introduction to Computational Biology. Maps, Sequences and Genomes
M.S. Waterman
Chapman & Hall, London, UK, 1995.