Bioinformatyk.eu nowy serwis o bioinformatyce i programowaniu

RNABuilder is a program for RNA 3D structure modeling. It allows the user to specify a set of constraints for base pairing and stacking, distance restraints, rigidifying portions of the molecule, and many more. In practice, these can be combined to thread a RNA chain to one or more structural templates, and relax the structure [...]

The main problem when trying to align RNA sequences is that their four bases can vary a lot more than in proteins (see comment below). Fortunately, when considering many sequences from the same family, one can find many sites at which two positions are correlated – when there is A + U in some sequences, [...]

The oldest and still most important field in RNA bioinformatics is predicting RNA secondary structures. The Vienna package is a set of command-line tools for basic tasks, like: RNAfold – predicts the 2D structure from a RNA sequence with the lowest energy using the Zuker algorithm. RNAsubopt – predicts several suboptimal 2D structures from a [...]

ModeRNA is a tool for comparative modeling of RNA structures. As an input it takes a known RNA structure to be used as a template, and an alignment between the target sequence to be modeled and the template sequence. Then, it carries out a series of operations such as copying the unchanged parts from the [...]