Summary
The paper presents an introduction to some of the problems in computational molecular biology (CMB) viewed from a logic programming (LP) perspective. Non-deterministic formal grammars are presented to define biologically interesting subsequences of DNA. Also presented are compact representations of ambiguities by directed acyclic graphs. Various problems in CMB are discussed; their solutions using dynamic programming, hidden Markov models, and inductive logic programming are briefly described. It is believed that a study of these and related problems can contribute to provide a new impetus to LP research and its extensions.
“Biology is so digital, and incredibly complicated, but incredibly useful …I can’t be as confident about computer science as I can about biology. Biology easily has 500 years of exciting problems to work on …”
Donald Knuth in an interview given on Dec. 1993 at the Computer Literacy Bookshops
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References
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Cohen, J. (1999). Computational Molecular Biology: A Promising Application Using LP and its Extensions. In: Apt, K.R., Marek, V.W., Truszczynski, M., Warren, D.S. (eds) The Logic Programming Paradigm. Artificial Intelligence. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-60085-2_12
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DOI: https://doi.org/10.1007/978-3-642-60085-2_12
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