DNA-Based Modelling of Parallel Algorithms

Abstract. The area of computational biology, is living a fast growth, fed with a revolution in DNA sequencing and technology of mapping. With these new technologies for manipulation of sequences, the relevance of finding efficient solution to the so-called computer intractable problems has also grown, because many problems involved in analyzing DNA belong to this class of problems. One approach to find such solutions is to use DNA itself to perform computations, taking advantage of the massive parallelism involved in operations that manipulate DNA sequences. This is what is studied in the area of DNA computing. This work proposes a formal model to represent the DNA structure and the operations performed in laboratory with it. This model can be used to analyze DNA-based algorithms, as well as for simulating such algorithms in a computer. We use graph grammars, a formal specification language, to model the DNA sequences and operations.