Exploring Life through Logic Programming: Logic Programming in Bioinformatics

This chapter provides a broad overview of how logic programming, and in particular Answer Set Programming, can be used to model and solve some popular and challenging classes of problems in the general domain of bionformatics. In particular, the chapter explores the use of ASP in Genomics studies, such as Haplotype inference and Phylogenetic inference, in Structural studies, such as RNA secondary structure prediction and Protein structure prediction, and in Systems Biology. The chapter offers a brief introduction to biology and bioinformatics and working ASP code fragments for the various problems investigated.