Partial words and a theorem of Fine and Wilf
Theoretical Computer Science
Handbook of Formal Languages
Partial words and a theorem of Fine and Wilf revisited
Theoretical Computer Science
Theory of Codes
Codes, Involutions, and DNA Encodings
Formal and Natural Computing - Essays Dedicated to Grzegorz Rozenberg [on occasion of his 60th birthday, March 14, 2002]
Algorithms for Testing That Sets of DNA Words Concatenate without Secondary Structure
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
Formal and natural computing
Coding properties of DNA languages
Theoretical Computer Science
Testing primitivity on partial words
Discrete Applied Mathematics
Theoretical Computer Science
Theoretical Computer Science
Graph connectivity, partial words, and a theorem of Fine and Wilf
Information and Computation
Overlap-freeness in infinite partial words
Theoretical Computer Science
Note: Testing avoidability on sets of partial words is hard
Theoretical Computer Science
Periodicity algorithms for partial words
MFCS'11 Proceedings of the 36th international conference on Mathematical foundations of computer science
Designing nucleotide sequences for computation: a survey of constraints
DNA'05 Proceedings of the 11th international conference on DNA Computing
DNA codes and their properties
DNA'06 Proceedings of the 12th international conference on DNA Computing
Abelian pattern avoidance in partial words
MFCS'12 Proceedings of the 37th international conference on Mathematical Foundations of Computer Science
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A very basic problem in all DNA computations is finding a good encoding. Apart from the fact that they must provide a solution, the strands involved should not exhibit any undesired behaviour, especially they should not form secondary structures. Various combinatorial properties like repetition-freeness and involution-freeness have been proposed to exclude such misbehaviour. Another option, which has been considered, is requiring a big Hamming distance between the codewords. We propose to consider partial words for the solution of the coding problem. They, in some sense, already include the Hamming distance in the definition of compatibility and are investigated for many combinatorial properties. Thus, they can be used to guarantee a desired distance and simultaneously other properties. As the investigations on partial words are attracting more and more attention, they might be able to provide an ever-growing toolbox for finding good DNA encodings.