What are the differences between RNASViewer and other RNA secondary structure prediction software?


Using SSDJ, SVG and JavaScript and C++, our RNASviewer web service consists of 3 separable steps, permitting plug-in, portability and extension. (1) We deployed the secondary structure prediction algorithms from RNAfold, RNAshapes and RNAsubopt that generate base-paring information in DBN format. (2) We implemented our own C++ program that utilizes DBN, CT and BPSEQ inputs and generates SSDJ outputs. (3) Using SSDJ outputs as inputs, we developed two drawing programs: one in C++ that creates high-quality, downloadable PNG images and the other in JavaScript that generates SVG images within a highly interactive web interface.

Our web service with such 3-step procedure is different from existing RNA secondary structure prediction tools such as RNAfold, RNAshapes, RNAsubopt and mFold, in which the steps of assigning graphic information to each base and drawing are essentially bundled together. The advantage of our 3-step procedure with SSDJ data format is to facilitate the modularity, comparability and compatibility among different RNA secondary structure prediction and drawing tools. For example, a program with an improved algorithm in folding prediction that can generate SSDJ outputs could use our highly interactive web interface to empower biologists in their RNA studies.


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