Bounds for DNA codes with constant GC-content

We derive theoretical upper and lower bounds on the maximum size of DNA codes of length n with constant GC-content w and minimum Hamming distance d, both with and without the additional constraint that the minimum Hamming distance between any codeword and the reverse-complement of any codeword be at least d. We also explicitly construct codes that are larger than the best previously-published codes for many choices of the parameters n, d and w.Comment: 13 pages, no figures; a few references added and typos correcte

Improved Lower Bounds for Constant GC-Content DNA Codes

The design of large libraries of oligonucleotides having constant GC-content and satisfying Hamming distance constraints between oligonucleotides and their Watson-Crick complements is important in reducing hybridization errors in DNA computing, DNA microarray technologies, and molecular bar coding. Various techniques have been studied for the construction of such oligonucleotide libraries, ranging from algorithmic constructions via stochastic local search to theoretical constructions via coding theory. We introduce a new stochastic local search method which yields improvements up to more than one third of the benchmark lower bounds of Gaborit and King (2005) for n-mer oligonucleotide libraries when n <= 14. We also found several optimal libraries by computing maximum cliques on certain graphs.Comment: 4 page

Group Divisible Codes and Their Application in the Construction of Optimal Constant-Composition Codes of Weight Three

The concept of group divisible codes, a generalization of group divisible designs with constant block size, is introduced in this paper. This new class of codes is shown to be useful in recursive constructions for constant-weight and constant-composition codes. Large classes of group divisible codes are constructed which enabled the determination of the sizes of optimal constant-composition codes of weight three (and specified distance), leaving only four cases undetermined. Previously, the sizes of constant-composition codes of weight three were known only for those of sufficiently large length.Comment: 13 pages, 1 figure, 4 table

The PBD-Closure of Constant-Composition Codes

We show an interesting PBD-closure result for the set of lengths of constant-composition codes whose distance and size meet certain conditions. A consequence of this PBD-closure result is that the size of optimal constant-composition codes can be determined for infinite families of parameter sets from just a single example of an optimal code. As an application, the size of several infinite families of optimal constant-composition codes are derived. In particular, the problem of determining the size of optimal constant-composition codes having distance four and weight three is solved for all lengths sufficiently large. This problem was previously unresolved for odd lengths, except for lengths seven and eleven.Comment: 8 page

Linear Size Optimal q-ary Constant-Weight Codes and Constant-Composition Codes

An optimal constant-composition or constant-weight code of weight $w$ has linear size if and only if its distance $d$ is at least $2w-1$. When $d\geq 2w$, the determination of the exact size of such a constant-composition or constant-weight code is trivial, but the case of $d=2w-1$ has been solved previously only for binary and ternary constant-composition and constant-weight codes, and for some sporadic instances. This paper provides a construction for quasicyclic optimal constant-composition and constant-weight codes of weight $w$ and distance $2w-1$ based on a new generalization of difference triangle sets. As a result, the sizes of optimal constant-composition codes and optimal constant-weight codes of weight $w$ and distance $2w-1$ are determined for all such codes of sufficiently large lengths. This solves an open problem of Etzion. The sizes of optimal constant-composition codes of weight $w$ and distance $2w-1$ are also determined for all $w\leq 6$, except in two cases.Comment: 12 page