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We describe how deletion-correcting codes may be enhanced to yield codes with double-strand DNA-sequence codewords. This enhancement involves abstractions of the pertinent aspects of DNA; it nevertheless ensures specificity of binding for all pairs of single strands derived from its codewords—the key desideratum of DNA codes– i.e. with binding feasible only… (More)

- A G D 'yachkov, V V Rykov
- 2013

A new lower bound for the length of disjunctive codes [I] is proved. An upper bound obtained by the method of random coding is given. columns (of 0 and 1) of length N. The componentwise Boolean sum u=u(1)Vu(2)V ... Vu(s) of columns u(l), u(2), ... , u(s) is what we call binary column u = (ul' u 2 , • • • , uN} whose components are defined by the expressions… (More)

Let [t] represent a nite population with t elements. Suppose we have an unknown d-family of k-subsets of [t]. We refer to as the set of positive k-complexes.I nt h egroup testing for complexes problem, must be identied by performing 0, 1 tests on subsets or pools of [t]. A pool is said to be positive if it completely contains a complex; otherwise the pool… (More)

DNA nanotechnology often requires collections of oligonucleotides called "DNA free energy gap codes" that do not produce erroneous crosshybridizations in a competitive muliplexing environment. This paper addresses the question of how to design these codes to accomplish a desired amount of work within an acceptable error rate. Using a statistical… (More)

We discuss the concept of t-gap block isomorphic subsequences and use it to describe new abstract string metrics that are similar to the Levenshtein insertion-deletion metric. Some of the metrics that we define can be used to model a thermodynamic distance function on single-stranded DNA sequences. Our model captures a key aspect of the nearest neighbor… (More)

We present a group testing approach to identify the first d vertices with the highest betweenness centrality. Betweenness centrality (BC) of a vertex is the ratio of shortest paths that pass through it and is an important metric in complex networks. The Brandes algorithm computes the BC cumulatively over all vertices. Approximate BC of a single vertex can… (More)