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FULL MATCHING AND ISOMORPHISM OF NUCLEOTIDE CHAINS

The structure of DNA/RNA chains is determined at several different levels. Although the primary sequence is fundamental in determining further properties, the higher level organization may have a backward influence. Beyond the physical structure of the chain, an abstract ’shape’ can also be defined. This is described in terms of relationships among the building blocks. We aim to show, that matching sequences are not exclusive representatives of relationships among nucleotide chains. Our approach is based on lattice theory, since lattice theory especially fits the problem. Beside the qualitative recognition of (algebraic) similarity, we also give a measure. This allows the structured quantification of the ’similarity distance’ of two chains. Such a decomposition provides the possibility to recognize relationships between biological phenomena and deep-lying structural similarities.