[] and {} would clash with representations of pseudoknots.
And <> would drive XML parsers crazy. Open to other options. Are there any existing conventions?
I’m not aware of any related to the nature (cis/trans) of the pairs, unless you’d be willing to work with groups of 3 characters, as in (c|t)(W|H|S)(W|H|S), for instance cWW, cHS, etc
cool one
Some Hexaloops to try:
nice - I see potential for a Cloud Lab.
Erh. Which bit is 5’ and which 3’?
Is the base ordering the same as EteRNA, so that (B) T-loop would be GUUCGAUCC as (…) or is it reversed: CCUAGCUUG? I haven’t yet got the 5’-3’ bit straight in my mind.
I believe the left side is 5’ and the right side 3’, when not marked, corresponding to the way we read English and the way RNA synthesizes naturally.
Yes, your first T-loop is correctly written. It is marked on the diagrams.
Twins in 3D but not in 2D. One has 2D pseudoknot & one has 2D dangle end.
Fascinating…
with numbers added to the 3D side; from Elnando’s wiki page on self-interacting sequences:
.png?1381192961)
.png?1381193251)