Efficient drawing of RNA secondary structure
نویسندگان
چکیده
منابع مشابه
Efficient drawing of RNA secondary structure
In this paper, we propose a new layout algorithm that draws the secondary structure of a Ribonucleic Acid (RNA) automatically according to some of the biologists’ aesthetic criteria. Such layout insures that two equivalent structures (or sub-structures) are drawn in a same and planar way. In order to allow a visual comparison of two RNAs, we use an heuristic that places the biggest similar part...
متن کاملVARNA: Interactive drawing and editing of the RNA secondary structure
DESCRIPTION VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases. FEATURES VARNA implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing as five picture formats, either pixel-based (JPEG, PNG) or vecto...
متن کاملA vector-based method for drawing RNA secondary structure
MOTIVATION To produce a polygonal display of RNA secondary structure with minimal overlap and distortion of structural elements, with minimal search for positioning them, and with minimal user intervention. RESULTS A new algorithm for automatically drawing RNA secondary structure has been developed. The algorithm represents the direction and space for a structural element using vector and vec...
متن کاملEfficient parameter estimation for RNA secondary structure prediction
MOTIVATION Accurate prediction of RNA secondary structure from the base sequence is an unsolved computational challenge. The accuracy of predictions made by free energy minimization is limited by the quality of the energy parameters in the underlying free energy model. The most widely used model, the Turner99 model, has hundreds of parameters, and so a robust parameter estimation scheme should ...
متن کاملRNA secondary structure design.
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure we want to find a sequence that has a certain structure as its ground state. If such a sequence exists, the structure is called designable. We have implemented a branch-and-bound algorithm that is able to do an exhaustive search within the sequence space, i.e., gives an exact...
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ژورنال
عنوان ژورنال: Journal of Graph Algorithms and Applications
سال: 2006
ISSN: 1526-1719
DOI: 10.7155/jgaa.00131