They serve numerous roles, from modulating gene expression to catalyzing reactions. These new ncRNA sequences range in size from microRNAs to Xist. The prediction of RNA structure has received increasing attention over the last decade as the number of known functional RNA sequences, called non-coding RNA (ncRNA), has increased. The package is available for download from the Mathews lab homepage at. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The original graphical user interface for Microsoft Windows is still maintained. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. RNAstructure is a software package for RNA secondary structure prediction and analysis. ![]() RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. ![]() The phosphate backbone (indicated by the curvy lines) is on the outside, and the bases are on the inside.To understand an RNA sequence's mechanism of action, the structure must be known. \): Native DNA is an antiparallel double helix.
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