mantelijo / bmol2d

Schematic RNA/DNA structures in 2D

BMol2D

Schematic RNA/DNA secondary structure visualization tool working entirely in your browser.

Samples

Some example structures

• 3Q1Q - my favorite structure
• 5B2R - my second favorite structure
• 6XRZ
• 6C0F - ribosomal subunit, might bet slow on some computers
• 2OM7
• 1H1K

Building project

Install npm_modules

yarn install

Compile wasm module

cd wasm/vienna-rna/ && ./compile_wasm.sh

To compile js assets

yarn build

Run locally

To run project locally, start the vite dev server with the following command:

yarn dev

If you wish to generate secondary structures for RNA molecules, see Seoncdary Structures.

Secondary structures

Dot-braket strings are used for generating secondary structure coordinates. Currently, dot-braket strings cannot be correctly generated in the browser environment and external dependencies are required. There are two ways to provide dot-braket strings for the app: by running included python script which will be queried for dot-braket automatically, or by providing the dot-braket strings manually (from servers such as RNAPDBee or other sources).

Python script for dot-braket structures

RNA secondary structures information generation currently uses Forgi Library v1.0 and requires globally available MC-Annotate executable with python3. Make sure you have these dependencies installed on your system. To start the secondary structure generator, run the following command:

python3 ./wasm/coordinates_server.py

This command will start a minimal python http.server on localhost:8001. This endpoint is queried for dot-braket structures which are later provided to the wasm module, which generates the secondary structure coordinates that are required to display RNA secondary structures.

MC-Annotate installation

MC-Annotate can be installed from MC-Annotate repository. It requires you to have mmcore library installed on your system and cmake. Once you have mccore installed, make sure to include the correct paths to mmcore library in MC-Annotate FindMCCORE.cmake. After MC-Annotate executable is built, symlink or add it to your path and make sure to name it exactly MC-Annotate as forgi library is calling it by this name.

Project structure

├── build - build directory
├── public - web assets
├── src - web app
└── wasm - naview algorithm extracted from ViennaRNA package and some other libraries used to generate secondary structures

Acknowledgments

• ViennaRNA
• MC-Annotate
• Forgi
• VU Department of Bioinformatics