While RNA primary structure describes solely the string of bases, RNA secondary structure includes local intra-molecular interactions between pairs of bases, which form weak hydrogen bonds. Two such bonded bases are called paired. Thus RNA secondary structure can be represented as a sequence of bases annotated with lines between paired bases. A more intuitive representation displays RNA seconda...

Ribonucleic acid (RNA) strings are strings over the four-letter alphabet {A, C, G, U} with a secondary structure of base-pairing between A U and C G pairs in the string 1 . Edges are drawn between two bases that are paired in the secondary structure and these edges have traditionally been assumed to be noncrossing. The noncrossing base-pairing naturally leads to a tree-like representation of th...

Ribonucleic acid (RNA) strings are strings over the four-letter alphabet fA; C; G; Ug with a secondary structure of base-pairing between A 0 U and C 0 G pairs in the string. Edges are drawn between two bases that are paired in the secondary structure and these edges have traditionally been assumed to be noncrossing. The noncrossing base-pairing naturally leads to a tree-like representation of t...

Ribonucleic acid (RNA) strings are strings over the four-letter alphabet fA;C;G;Ug with a secondary structure of base-pairing between A U and C G pairs in the string 1 . Edges are drawn between two bases that are paired in the secondary structure and these edges have traditionally been assumed to be noncrossing. The noncrossing base-pairing naturally leads to a tree-like representation of the s...

RNA secondary structure prediction is a fundamental problem in structural bioinformatics. The prediction problem is difficult because RNA secondary structures may contain pseudoknots formed by crossing base pairs. We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots. An RNA secondary structure is k-partite if it is the union of k ps...

Background: RNA molecules play many important regulatory, catalytic and structural <span style="font-variant: normal; font-style: norma...

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and in...

mRNA secondary structure can be an important determinant of the efficiency of translation initiation. To study the effect of secondary structure on translation initiation, in vitro secondary structure analysis was performed on 32 lacZ RNA transcripts that differ in their in vivo translation initiation efficiencies because of mutations. We have shown that well-translated RNA has a relatively uns...

The recent interest in function of various RNA structures, reflected in the growth of solved RNA structures in PDB, calls for methods for effective and efficient similarity search in RNA structural databases. Here, we propose a method called SETTER (RNA SEcondary sTructurebased TERtiary structure similarity) based on partitioning of RNA structures into so-called generalized secondary structure ...

RNAs play an important role in bioinformatic applications. Their ability to serve not only as information carrier, but also to develop catalytic properties highlights them in the set of organic macromolecules notably. As these catalytic properties are closely related to the three-dimensional configuration (tertiary structure) of the RNA molecule, the formation and prediction of this tertiary st...