Hello,
As the developers of the RNAcanvas web app for 2D RNA structure visualization, we would like to inquire about the idea of adding links to RNAcanvas to the mfold / UNAfold website for predicted structures.
For example, a predicted structure with:
Sequence "AGCGCUAUCUCAAAUGGACACUCCGCAACCAUGGCGUCGCCUCCUGCAAAGAAUUGUCAUAUGAGUAUGAGGUUGUUGGC"
Secondary structure ".(((((((......(((.....))).....))))))).(((((.(((.................))).)))))......."
(in dot-bracket / "Vienna" / Shapiro format)
...is linked to by the following URL, utilizing the "sequence" and "dot_bracket" URL parameters, respectively:
https://code.rnacanvas.app/?sequence=AGCGCUAUCUCAAAUGGACACUCCGCAACCAUGGCGUCGCCUCCUGCAAAGAAUUGUCAUAUGAGUAUGAGGUUGUUGGC&dot_bracket=.(((((((......(((.....))).....))))))).(((((.(((.................))).))))).......
Simply including this link on a website (e.g., mfold / UNAfold) would allow a user to open the predicted structure in RNAcanvas.
RNAcanvas provides:
1. Advanced functionality for controlling the layout of a drawing, including the ability to click-and-drag bases, rotate bases (while keeping their letters upright), arrange bases according to their secondary structure, and apply the RNAcanvas untangling algorithm. See the Layout form (openable via the "Layout" button in the bottom-left Toolbar) for the full layout functionality.
2. The ability to easily add / remove base-pairs. Pairing bases is bound to the [ P ] key and unpairing bases is bound to the [ U ] key. The Pair / Unpair buttons of the Toolbar can also be used.
3. The ability to stylize / outline bases, using the Editing form (openabled via the "Edit" button of the Toolbar).
4. Undo / redo functionality - bound to the [ Ctrl+Z ] / [ Shift+Ctrl+Z ] keys and also the "Undo" / "Redo" buttons of the Toolbar.
5. The ability to save one's drawing as a file for later use. Drawings can be downloaded in RNAcanvas format by pressing [ Ctrl+S ] or using the top-left "Save" button. Drawing files can be stored on one's computer and reopened in RNAcanvas at a later time.
6. The ability to export the drawing in SVG format, by pressing [ E ] or using the Export form (accessible via the top-left "Export" button). Exported SVG files can be opened in vector graphics editors such as Inkscape and Illustrator, which allow one to make further edits and export one's drawing in many more picture formats.
RNAcanvas can also be directly embedded in other websites (see the Github docs https://pzhaojohnson.github.io/rnacanvas.embedded/ and live CodePen example https://codepen.io/pzjohnson/pen/xxoKvGp).
We aspire for RNAcanvas to become the default 2D RNA structure viewer component across the web (similar to what JSmol is for 3D structures).
The previous version of RNAcanvas was published in NAR ~2 years ago: https://doi.org/10.1093/nar/gkad302
RNAcanvas is also linked to by the R2DT RNA structure suite (recent NAR paper: https://doi.org/10.1093/nar/gkaf032).
We're eager to receive any feedback regarding this proposal. Thank you!