Nucleic acid secondary structure plays an important role in nucleic acid-nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have n...

In this paper, we tackle the problem of the prediction by energy computation of RNA stable secondary structures. We present, under the Hypothesis of Loops Dependent Energy (HLDE), our dynamic programming algorithm to compute the free energies of the stable secondary structures and our traceback algorithm to predict these structures. We compute the free energies of the stable secondary structure...

A tree similarity algorithm for RNA (ribonucleic acid) secondary structure comparison is presented. The elements (nucleotides and nucleotide-pairs) of an RNA secondary structure are represented as normalized node-weighted trees. We show that our weighted tree representations of RNA secondary structures are informative and useful. Based on this unique representation for RNA secondary structure, ...

Summary: We present a web server dedicated to the comparison of RNA secondary structures. This server allows to compare pairs of RNA secondary structures and to search, for a given RNA secondary structure, RNA genes with similar structures in a large database of RNA structures. The comparison and search are performed using an edit distance algorithm that considers a wide range of edit operation...

Introduction Traditional architectures which consist of a single processor, a small main memory, and secondary memory devices (e.g. disks), are gradually being replaced by multiprocessor multi-disk architec­ tures with a relatively large main m~mory. The processors either reside in the same site and communicate via the shared memory, or reside in different sites and communicate via a local netw...

The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the ...

in this study, the effect of the secondary structure of the protein on the acid strength of three structures of random (r), alpha helix (α) and beta sheet (b) were investigated theoretically. these structures are related to the cationic amino acids of histidine and lysine in the polypeptide chain of eight-glycine residue. computational methods at the hf, b3lyp, x3lyp and m05-2x levels in the ga...

This commentary presents a conceptual framework, Quality in the Continuum of Cancer Care (QCCC), for quality improvement studies and research. Data sources include review of relevant literature (cancer care, quality improvement, organizational behavior, health services evaluation, and research). The Detecting Early Tumors Enables Cancer Therapy (DETECT) project is used to apply the QCCC model t...

This case study examines an organization which is partnering to provide ICT solutions for secondary schools in Uganda. Based on interviews and observation, we identify nine key transitions in this organization’s development. Each transition is characterized by a challenge that was faced and a solution that was implemented or attempted. We draw broader “lessons learned” from the results to infor...