Foreword

Sorin Istrail, Pavel Pevzner, Ron Shamir
2000 Discrete Applied Mathematics  
Foreword This is the third special volume of Discrete Applied Mathematics focusing on development of new combinatorial techniques in computational molecular biology. The ÿrst and the second special volumes were published in 1996 and 1998 and launched the Computational Molecular Biology Series (DAM-CMB Series). The third volume of the DAM-CMB Series contains a multitude of papers in such areas as DNA mapping and sequencing, DNA sequence analysis, and protein and RNA structure analysis. Mapping
more » ... d sequencing: The paper "Probe locations in the presence of errors: a problem from DNA mapping" by B. Mumey is motivated by uorescence in situ hybridization (FISH) experiments. The corresponding combinatorial problem is to ÿnd the positions of points on a line that satisfy some constraints on pairwise distances between points (probe-location problem). The author proposes a randomized algorithm for this problem and describes the results of tests on human chromosome 4. The paper "Partitioning single molecule maps into multiple populations: algorithms and probabilistic analysis" by L. Parida and B. Mishra is motivated by the optical mapping technology. The authors study the problem of partitioning the set of molecules (optical mapping data) into K populations so that each restriction site for a population is supported by "enough" restriction sites in the same population. The paper "Inverse inbreeding coefÿcient problems with an application to linkage analysis of recessive deseases in inbred populations" by R. Agarwala, L.G. Biesecker, and A.A. Scha er considers the problem of family tree reconstruction. The existing genetic-mapping algorithms are not well suited to large imbred pedigrees and the authors study a question of extracting a small pedigree from genealogy and preserving the likely paths of disease gene inheritance. The paper "Statistical learning formulation of the DNA base-calling problem and its solution in a Bayesian EM framework" by M.S. Pereira, L. Andrade, S.E. Difrawy, B.L. Karger, and E.S. Manolakos is motivated by DNA sequencing. The authors propose a new formulation of the base-calling problem that is crucial for improving accuracy of DNA sequencing. The experimental results indicate that the proposed algorithm often exceeds the accuracy of commercially available software. DNA sequence analysis: The paper "A Polyhedral approach to sequence alignment problem" by J.D. Kececioglu, H.P. Lenhof, K. Melhorn, P. Mutzel, K. Reinert and M. Vingron proposes a new polyhedral approach to the classical sequence alignment problem. Sequence alignment is reformulated in terms of integer programming thus allowing the studies of the corresponding polytopes. The authors prove the duality theorems for some of these polytopes and solve them in polynomial time. The proposed method may be able to solve the instances of multiple alignment problem that are 0166-218X/00/$ -see front matter ? 2000 Elsevier Science B.V. All rights reserved. PII: S 0 1 6 6 -2 1 8 X ( 0 0 ) 0 0 1 9 9 -2
doi:10.1016/s0166-218x(00)00255-9 fatcat:cbst4oy6iveubnmwlas5x255r4