The following papers have been accepted for the third special issue in the Computational Biology series of Discrete Applied Mathematics: R. Agarwala, L. G. Biesecker, and A. A. Schaffer Inverse inbreeding coefficient problems with an application to linkage analysis of recessive deseases in inbred populations T. Akutsu Dynamic programming algorithm for RNA secondary structure prediction with pseudoknots R.Arratia, B. Bollobas, D. Coppersmith, G. B. Sorkin Euler circuits and DNA sequencing by hybridization B. Berger, J. King, R. Schwartz, and P. W. Shor Local rule mechanism for selecting icosahedral shell geometry R. Bundschuh and T. Hwa An analytic study of the phase transition line in local sequence alignment with gaps J.D. Kececioglu, H.P. Lenhof, K. Melhorn, P. Mutzel, K. Reinert, M.Vingron, A polyhedral approach to sequence alignment problems B. Mumey Probe location in the presence of errors: a problem from DNA mapping L. Parida and B. Mishra. Partitioning single molecule maps into multiple populations: algorithms and probabilistic analysis M. S. Pereira, L. Andrade, S. E. Difrawy, B. L. Karger, and E. S. Manolakos Statistical learning formulation of the DNA base-calling problem and its solution in a Bayesian EM framework M. Regnier A unified approach to word occurrence probabilities L. Wang, B. Ma, and M. Li Fixed topology alignment with recombination