I started a new thread called Modular RNA using Junctures coupled with Index and Search that relates to this thread. It proposes constructing a database of substructures based on using 3-pair stack ends that act as junctures between stacks and “fobs”. The database would be populated using RNA sequences with known secondary structures from PDB, the EteRNA lab results, and elsewhere.
It seemed a different enough idea to warrant a new thread, but related enough to be worth mentioning here.
@ jpbida - Is RSIM assembling fragments only for tertiary structure prediction? If so, do you think the approach could be extended to inverse folding as well? Some of the challenges look like you’re doing both.
@ tsuname - It may be useful to add some more specific search options, especially with so many new sequences about to be synthesized. For example, allow searching by the size of bulges, the number of unpaired bases in hairpins, the dimensions of internal loops, the distribution of branches in multiloops, etc. Then it would be possible to very quickly search for all RNAs with a 2x2 loop (or some other desired element).
@Quasispecies - my thread on Modular RNA poses one possibility in that regard. It breaks a structure into segments which could then be classified by shape/size. Then you could index back to the full sequence/structure.
Hi,
This is an exciting project, and it would be great to get an update on how things are going with it.
Regards,
Merryskies