maxieds
commented
4 years ago Since we already have Vienna as a prerequisite library for the radial layout viewer, we might as well look into supporting FASTA formats using the Vienna Boltzmann sampling algorithms. See:
- https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/groupsuboptstochbt.html#ga596ed9bcd86f629a7c7c59c58b297db5
- https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/grouppartfunc__global.html#ga29e256d688ad221b78d37f427e0e99bc
- https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/groupfoldcompound.html#ga576a077b418a9c3650e06f8e5d296fc2
- https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/groupfoldcompound.html#gga01a4ff86fa71deaaa5d1abbd95a1447dab821ce46ea3cf665be97df22a76f5023
- https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/examples_c.html#ex_c_fc
Note that we already require integration with the ViennaRNA library to draw the radial layout diagrams. So at least partial support for this optional feature is easy.
This feature would allow users to load sequences from stock, vanilla FASTA and TXT files containing just the base / nucleotide sequence data. Then we could have an option to call a sampling generation routine, e.g., from Vienna, to generate say n=20 unique structures on-the-fly for use with RNAStructViz. This might expand the use cases for many users, and would be, I think, nice to have if we can test it and get this functionality working well by default out-of-the-box.
Optional, compile-time linking with alternate sampling utilities, like those from RNAStructure or RNAFold, could later be added. Though this complicates the build process. I suggest we start with Vienna sampling support since this library is already there and configured for our build time purposes.