References

Corpet F. and Michot B. (1994) RNAlign program: alignment of RNA sequencess using both primary and secondary structures. Comput. Appl. Biosci. 10:389-399.

Eddy S.R. and Durbin R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res. 22:2079-2088.

Gorodkin J., Heyer L.J. and Stormo G.D. (1997) Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res. 25:3724-3732.

Lenhof H.-P, Reinert K. and Vingron M. (1998) A polyhedral approach to RNA sequence structure alignment. In Proc. of the First Annual International Conference on Computational Molecular Biology RECOMB 98, p 153-162, S. Istrail, P. Pevzner and M.S. Waterman eds. ACM Press.

Nemhauser G.L. and Trotter L.E. (1975) Properties of vertex packing and independence system polyhedra. Mathematical Programming 6:48-61.

Nemhauser G.L. and Wolsey L.A. (1988) Integer and Combinatorial Optimization. Wiley.

Reinert K., Lenhof H.-P., Mutzel P. Melhorn K. and Kececioglu J. (1997) A branch and cut algorithm for multiple sequence alignment. In Proc. of the First Annual International Conference on Computational Molecular Biology RECOMB 97, p 241-249, S. Istrail, P. Pevzner and M.S. Waterman eds. ACM Press.

Sankoff D. (1985) Simultaneous solution of the RNA folding, alignment and protosequences problem. SIAM J. on Appl. Math. 45:810-825.

Tsukiyama S., Ide M. and Ariyoshi H. (1977) A new algorithm for generating all the maximal independent sets. SIAM J. on Computing 45:810-825.

Waterman M.S. (1989) Consensus methods for folding single-stranded nucleic acids. In Mathematical Methods for DNA Sequences, p 185-224, M.S. Waterman ed. CRC Press.

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