Abstract
This work presents an algorithm for constructing artificial DNA libraries that consist of chains having minimal tendency to hybridize with each other. Such libraries can be applied in DNA computing (Adleman, 1994) for encoding problem instances. The algorithm is based on an extension of de Bruijn graphs and de Bruijn sequences. In general, the algorithm can be used to build a chain over any alphabet of even size with defined binary symmetric irreflexive relation of complementarity — the obtained chain is a modified de Bruijn sequence with shifted windows (there are no repetitive k-long subchains that start on positions divisible by a given parameter) where half of these windows are removed to eliminate relation of complementarity among them.
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