Showing papers by "Kalpana Mahalingam published in 2003"

Languages of DNA Based Code Words

Abstract: The set of all sequences that are generated by a biomolecular protocol forms a language over the four letter alphabet Δ={A,G,C,T}. This alphabet is associated with a natural involution mapping θ, A↦ T and G↦ C which is an antimorphism of Δ*. In order to avoid undesirable Watson-Crick bonds between the words (undesirable hybridization), the language has to satisfy certain coding properties. In this paper we build upon the study initiated in [11] and give necessary and sufficient conditions for a finite set of “good” code words to generate (through concatenation) an infinite set of “good” code words with the same properties. General methods for obtaining sets of “good” code words are described. Also we define properties of a splicing system such that the language generated by the system preserves the desired properties of code words.

Methods for Constructing Coded DNA Languages

Abstract: The set of all sequences that are generated by a biomolecular protocol forms a language over the four letter alphabet Δ={A,G,C,T}. This alphabet is associated with a natural involution mapping θ, A↦T and G↦C which is an antimorphism of Δ*. In order to avoid undesirable Watson-Crick bonds between the words (undesirable hybridization), the language has to satisfy certain coding properties. In this paper we build upon an earlier initiated study and give general methods for obtaining sets of code words with the same properties. We show that some of these code words have enough entropy to encode {0,1}* in a symbol-to-symbol mapping.