A logic-based approach to polymer sequence analysis

Polymers are compounds formed by the joining of smaller, often repeating, units linked by covalent bonds. The analysis of their sequence is a fundamental issue in many areas of chemistry, medicine and biology. Nowadays, the prevalent approach to this problem consists in using a mass spectrometry analysis that gives information about the molecular weights of the polymer and of its fragments. This information should be used in order to obtain the sequence. This is however a difficult mathematical problem, and several approaches have been proposed for it. In particular, a promising one is based on a propositional logic modeling of the problem. This paper presents conceptual improvements in this approach, principally the off-line computation of a database that substantially speeds-up the sequencing operations. This is obtained by finding a correspondence between sequences and natural numbers, so that all sequences up to a certain molecular weight can be implicitly considered in the above database, and explicitly computed only when needed. Results on real-world problems show the effectiveness of this approach.