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

On Critical Relative Distance of DNA Codes for Additive Stem Similarity

We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the "hybridization potential" of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a thermodynamically motivated similarity measure called an additive stem similarity. These results yield a method to analyze and compare known samples of the nearest neighbor "thermodynamic weights" associated to stacked pairs that occurred in DNA secondary structures.Comment: 5 or 6 pages (compiler-dependable), 0 figures, submitted to 2010 IEEE International Symposium on Information Theory (ISIT 2010), uses IEEEtran.cl

DNA Codes Based on Stem Similarities Between DNA Sequences

DNA codes consisting of DNA sequences are necessary for DNA computing. The minimum distance parameter of such codes is a measure of how dissimilar the codewords are, and thus is indirectly a measure of the likelihood of undetectedable or uncorrectable errors occurring during hybridization. To compute distance, an abstract metric, for example, longest common subsequence, must be used to model the actual bonding energies of DNA strands. In this paper we continue the development [1,2,3] of similarity functions for q-ary n-sequences The theoretical lower bound on the maximal possible size of codes, built on the space endowed with this metric, is obtained. that can be used (for q = 4) to model a thermodynamic similarity on DNA sequences. We introduce the concept of a stem similarity function and discuss DNA codes [2] based on the stem similarity. We suggest an optimal construction [2] and obtain random coding bounds on the maximum size and rate for such codes

Subwords in reverse-complement order

We examine finite words over an alphabet $Gamma={a,bar{a};b,bar{b}}$ of pairs of letters, where each word $w_1w_2...w_t$ is identical with its {it reverse complement} $bar{w_t}...bar{w_2}bar{w_1}$ (where $bar{bbar{a}}=a,bar{bar{b}}=b$). We seek the smallest $k$ such that every word of length $n,$ composed from $Gamma$, is uniquely determined by the set of its subwords of length up to $k$. Our almost sharp result ($ksim 2n/3$) is an analogue of a classical result for ``normal\u27\u27 words. This classical problem originally was posed by M.P. Sch"utzenberger and I. Simon, and gained a considerable interest for several researchers, foremost by Vladimir Levenshtein. Our problem has its roots in bioinformatics

Characterisation of two morphogenesis mutants in Arabidopsis thaliana

In this thesis is described the characterisation of two morphogenesis mutants of Arabidopsis thaliana, with the aim of furthering our understanding of signalling in development. A thorough phenotypic analysis of both mutants is presented, with particular attention paid to the seedling root. The results of genetic analysis of hydra2 are also presented. The hydra mutants are characterised by a pleiotropic phenotype, with defective embryonic and seedling cell patterning, morphogenesis and root growth. The HYDRA1 gene encodes a A8-A7 sterol isomerase, while HYDRA2 encodes a sterol C14 reductase, previously identified as the FACKEL gene product. Seedlings mutant for each gene are similarly defective in the concentrations of the three major Arabidopsis sterols. Reporter gene analysis showed mis-expression of the hormonally-regulated DR5, IAA2 and ACSl promoters and of the epidermal cell file-specific GL2 promoter in the mutants. The mutants also exhibit enhanced responses to auxin. The phenotypes can be partially rescued by inhibition of auxin and ethylene signalling, but not by exogenous brassinosteroids. Evidence of abnormal activity of hormone-related membrane-bounds proteins and of altered membrane permeability to auxin is presented. A model in which correct sterol profiles are required for regulated auxin and ethylene signalling through effects on membrane function is proposed