extended dot-bracket notation

[brendanf]

I'm working on a BioConductor package to interface with Infernal, which produces RNA alignments with an extended dot-bracket notation called WUSS. In addition to the characters allowed by Structstrings currently, WUSS allows:

for unpaired positions:
_    hairpin loops
-    bulges, internal loops
,    multifurcation loops
:    external residues
~    unaligned residues

for paired positions:
A-Z    left part of pseudoknot
a-z    right part of pseudoknot

At the moment I am just using BString and BStringSet to represent these secondary structure strings, but it seems that it would be useful to modify or extend Structstrings to also support WUSS. Is that something you would be interested in either a) implementing yourself, or b) considering a pull request for?

[FelixErnst]

@brendanf
Sorry for the long delay. Certainly a pull request would be much appreciated.

[FelixErnst]

Just had a look at the Infernal userguide. My guess would be that the following things would be on the todo list

• WUSSString classes implementation
• WUSSDataFrame classes implementation
• Figure out the overlap between DotBracketString classes and the WUSSString classes to decide whether it makes sense to implement a common StructString class ancestor
• Same for the the WUSSDataFrame classes and the DotBracketDataFrame classes