TYPE IV Biological and Bioinformatics Problems

Some bioinformatics problems can be formulated as MOOPs, for instance the sequence alignment of DNA or protein sequences, protein structure prediction and design, and inference of gene regulatory networks, just to mention a few. The interested reader is referred to the review of Handl et al. (2007) that covers in detail more MOO applications in bioinformatics. The next few paragraphs describe some of the current applications in bioinformafics of interest to the chemical engineering community. 

Sequence and structure alignment. Malard et al. (2004) formulate the de novo peptide identification as a constrained MOOP. The objectives considered in the study were the maximization of the similarity between portions of two peptides, and the maximization of the likelihood ratio between the null hypothesis and the alternative hypothesis. 

Calender et al. (2006) address the problem of identifying gene modules on the basis of different types of biological data such as gene expression and protein-protein interaction data. Module identification refers to the identification of groups of genes similar with respect to its function or regulation mechanism. 

Protein and structure prediction. Chen et al. (2005) proposed a method to solve the structure alignment problem for homologous proteins. This problem can be formulated as a MOOP where the objectives are maximize the number of aligned atoms and minimize their distance. 

Shin et al. (2005) use the controlled NSGA-II (Deb and Goel, 2001) to generate a set of quality DNA sequences. In this study, the quahty of a sequence was achieved by minimizing four objectives the similarity between two sequences in the set, the possible hybridization between sequences in a set, the continuous occurrence of the same base and the possible occurrence of the complementary substring in a sequence. 

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