Preventing Undesirable Bonds Between DNA Codewords

Kari, Lila; Konstantinidis, Stavros; Sosík, Petr

doi:10.1007/11493785_16

Cited by 9 publications

(7 citation statements)

References 14 publications

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“…For instance, the elasticity of DNA requires that codes must disallow multiple portions of a single code to bond [31,32], while chemistry requires that the codes must have balanced occurrences of letters A, T and G, C [33,34,35]. On the other hand, dipole codes have only a single pair of bonding letters, and inconsistency of mesoscale mixing allows codes to bond with even a single dipole pair [14].…”

Section: Introductionmentioning

confidence: 99%

Dipole codes attractively encode glue functions

Ipparthi

Mastrangeli

Winslow

2017

Theoretical Computer Science

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Dipole words are sequences of magnetic dipoles, in which alike elements repel and opposite elements attract. Magnetic dipoles contrast with more general sets of bonding types, called glues, in which pairwise bonding strength is specified by a glue function. We prove that every glue function g has a set of dipole words, called a dipole code, that attractively encodes g: the pairwise attractions (positive or non-positive bond strength) between the words are identical to those of g. Moreover, we give such word sets of asymptotically optimal length. Similar results are obtained for a commonly used subclass of glue functions.

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Section: Introductionmentioning

confidence: 99%

Dipole codes attractively encode glue functions

Ipparthi

Mastrangeli

Winslow

2017

Theoretical Computer Science

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“…introduced a theoretical approach to the problem of designing code words. Theoretical properties of languages that avoid certain undesirable hybridizations were discussed in [14,16,18]. Based on these ideas and code-theoretic properties, a computer program for generating code words is being developed [13,20].…”

Section: Introductionmentioning

confidence: 99%

DNA Codes and Their Properties

Kari

Mahalingam

2006

DNA Computing

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One of the main research topics in DNA computing is associated with the design of information encoding single or double stranded DNA strands that are "suitable" for computation. Double stranded or partially double stranded DNA occurs as a result of binding between complementary DNA single strands (A is complementary to T and C is complementary to G). This paper continues the study of the algebraic properties of DNA word sets that ensure that certain undesirable bonds do not occur. We formalize and investigate such properties of sets of sequences, e.g., where no complement of a sequence is a prefix or suffix of another sequence or no complement of a concatenation of n sequences is a subword of the concatenation of n + 1 sequences. The sets of code words that satisfy the above properties are called θ-prefix, θ-suffix and θintercode respectively, where θ is the formalization of the Watson-Crick complementarity. Lastly we develop certain methods of constructing such sets of DNA words with good properties and compute their informational entropy.

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“…The scope of the studied sequential insertion/deletion operations include insertion, shuffle, literal shuffle, deletion, bipolar deletion, scattered deletion, as well as their iterated and regulated versions. Recently, the applications of such language equations were shown in the coding theory for modelling noisy channels [8] or in the biocomputing research for characterization of sets of codewords for DNA computing [9,10].…”

Section: Introductionmentioning

confidence: 99%

“…Its importance and utility became more obvious in 2003 when the inverse operation, the deletion on trajectories was independently introduced in [1,13]. Several new results have been obtained since these two reports, some rather theoretical [2][3][4], some involving applications [9][10][11].…”

Section: Introductionmentioning

confidence: 99%

Aspects of shuffle and deletion on trajectories

Kari

Sosík

2005

Theoretical Computer Science

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Word and language operations on trajectories provide a general framework for the study of properties of sequential insertion and deletion operations. A trajectory gives a syntactical constraint on the scattered insertion (deletion) of a word into(from) another one, with an intuitive geometrical interpretation. Moreover, deletion on trajectories is an inverse of the shuffle on trajectories. These operations are a natural generalization of many binary word operations like catenation, quotient, insertion, deletion, shuffle, etc. Besides they were shown to be useful, e.g. in concurrent processes modelling and recently in biocomputing area.We begin with the study of algebraic properties of the deletion on trajectories. Then we focus on three standard decision problems concerning linear language equations with one variable, involving the above mentioned operations. We generalize previous results and obtain a sequence of new ones. Particularly, we characterize the class of binary word operations for which the validity of such a language equation is (un)decidable, for regular and context-free operands.

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Preventing Undesirable Bonds Between DNA Codewords

Cited by 9 publications

References 14 publications

Dipole codes attractively encode glue functions

Dipole codes attractively encode glue functions

DNA Codes and Their Properties

Aspects of shuffle and deletion on trajectories

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