A. Arslan, Regular expression constrained sequence alignment, Journal of Discrete Algorithms, vol.5, issue.4, pp.647-661, 2007.
DOI : 10.1016/j.jda.2007.01.003

A. Arslan and O. Egecioglu, ALGORITHMS FOR THE CONSTRAINED LONGEST COMMON SUBSEQUENCE PROBLEMS, International Journal of Foundations of Computer Science, vol.16, issue.06, pp.1099-1110, 2005.
DOI : 10.1142/S0129054105003674

A. Bairoch, The PROSITE dictionary of sites and patterns in proteins, its current status, Nucleic Acids Research, vol.21, issue.13, p.3097, 1993.
DOI : 10.1093/nar/21.13.3097

M. Bern and P. Plassmann, The Steiner problem with edge lengths 1 and 2, Information Processing Letters, vol.32, issue.4, pp.171-176, 1989.
DOI : 10.1016/0020-0190(89)90039-2

Y. Chen and K. Chao, On the generalized constrained longest common subsequence problems, Journal of Combinatorial Optimization, vol.21, issue.1, 2009.
DOI : 10.1007/s10878-009-9262-5

Y. Chung, W. Lee, and C. Tang, RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints, Nucleic Acids Research, vol.35, issue.Web Server, p.639, 2007.
DOI : 10.1093/nar/gkm275

Y. Chung, C. Lu, and C. Tang, Efficient algorithms for regular expression constrained sequence alignment, Information Processing Letters, vol.103, issue.6, pp.240-246, 2007.
DOI : 10.1016/j.ipl.2007.04.007

I. Dinur and S. Safra, On the hardness of approximating vertex cover, Annals of Mathematics, vol.162, issue.1, pp.439-486, 2005.
DOI : 10.4007/annals.2005.162.439

L. Foulds, G. , and R. , The steiner problem in phylogeny is NP-complete, Advances in Applied Mathematics, vol.3, issue.1, p.299, 1982.
DOI : 10.1016/S0196-8858(82)80004-3

V. Geffert, Translation of binary regular expressions into nondeterministic ??-free automata with O(nlogn) transitions, Journal of Computer and System Sciences, vol.66, issue.3, pp.451-472, 2003.
DOI : 10.1016/S0022-0000(03)00036-9

Z. Gotthilf, D. Hermelin, and M. Lewenstein, Constrained LCS: Hardness and Approximation, Lect. Notes Comput. Sci, vol.5029, pp.255-262, 2008.
DOI : 10.1007/978-3-540-69068-9_24

J. Hromkovi?c, S. Seibert, and T. Wilke, Translating Regular Expressions into Small ??-Free Nondeterministic Finite Automata, Journal of Computer and System Sciences, vol.62, issue.4, pp.565-588, 2001.
DOI : 10.1006/jcss.2001.1748

C. Iliopoulos and M. Rahman, New efficient algorithms for the LCS and constrained LCS problems, Information Processing Letters, vol.106, issue.1, pp.13-18, 2008.
DOI : 10.1016/j.ipl.2007.09.008

W. Jia, B. Han, and P. Au, Optimal multicast tree routing for cluster computing in hypercube interconnection networks, IEICE Trans. Inform. Syst, pp.87-1625, 2004.

X. Lin and L. Ni, Multicast communication in multicomputer networks, IEEE Transactions on Parallel and Distributed Systems, vol.4, issue.10, pp.1105-1117, 1993.
DOI : 10.1109/71.246072

Z. Peng and H. Ting, Time and Space Efficient Algorithms for Constrained Sequence Alignment, Lect. Notes Comput. Sci, vol.3317, pp.237-246, 2005.
DOI : 10.1007/978-3-540-30500-2_22

J. Savage, An Algorithm for the Computation of Linear Forms, SIAM Journal on Computing, vol.3, issue.2, pp.150-158, 1974.
DOI : 10.1137/0203011

G. Schnitger, Regular Expressions and NFAs Without ??-Transitions, Lect. Notes Comput. Sci, vol.3884, p.432, 2006.
DOI : 10.1007/11672142_35

J. Seberry and M. Yamada, Hadamard matrices, sequences, and block designs, Contemporary Design Theory: A Collection of Surveys, pp.431-560, 1992.

S. Sheu, Y. , and C. , Multicast Algorithms for Hypercube Multiprocessors, Journal of Parallel and Distributed Computing, vol.61, issue.1, pp.137-149, 2001.
DOI : 10.1006/jpdc.2000.1668

W. Shi and C. Su, The Rectilinear Steiner Arborescence Problem Is NP-Complete, SIAM Journal on Computing, vol.35, issue.3, pp.729-740, 2006.
DOI : 10.1137/S0097539704371353

T. Smith and M. Waterman, Identification of common molecular subsequences, Journal of Molecular Biology, vol.147, issue.1, pp.195-197, 1981.
DOI : 10.1016/0022-2836(81)90087-5

S. Sunyaev, G. Bogopolsky, and N. Oleynikova, From analysis of protein structural alignments toward a novel approach to align protein sequences, Proteins: Structure, Function, and Bioinformatics, vol.39, issue.3, pp.569-582, 2004.
DOI : 10.1002/prot.10503

J. J. Sylvester, Thoughts on inverse orthogonal matrices, simultaneous sign successions, and tessellated pavements in two or more colours, with applications to Newton's rule, ornamental tile-work and the theory of numbers, Philosophical Magazine and Journal of Science, vol.34, pp.461-475, 1867.

C. Tang, C. Lu, and M. Chang, Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment, Journal of Bioinformatics and Computational Biology, vol.01, issue.02, pp.267-287, 2003.
DOI : 10.1142/S0219720003000095

Y. Tsai, The constrained longest common subsequence problem, Information Processing Letters, vol.88, issue.4, pp.173-176, 2003.
DOI : 10.1016/j.ipl.2003.07.001