![]() ![]() Compensating base pair changes demonstrate the conservation of structure in spite of sequence not being conserved, for example a GC base pair in one sequence being replaced by a homologous AU pair in another sequence. In comparative analysis, base pairs are determined when they are conserved in multiple sequences and instances of compensating base pair changes occur. Secondary structure, defined as the set of canonical base pairs (AU, GC, and GU), can be determined using comparative analysis if a large number of sequences are available. One of the first steps to understanding the mechanism of action of an RNA is to determine its structure. 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. To understand an RNA sequence's mechanism of action, the structure must be known. ![]()
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