BackofenLab
[helix-based] optimize bulge breakpoint
I found an example where a shift of a one-sided bulge causes a significant energy change (in --mode=H)
--> IntaRNA -q GCUGAAAAACAUAACCCAUAAAAUGCUAGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUUUUU -t CUGGAUGAAUGACAGGGAAAACAUGCGUAAUACUUACGCAGUUCUCUGAAAAAGUGAUUUAAAUUUAGAUGGAUAGCGGUGUAUGGAAACGUUCUGUUACAUGAAAUGGCCCGUUAGACAUCACAAAUCGCGAAGAGUUUCCCAUUAAUUUUUGAUAUAUUUAAAACUUAGGACUUAUUUGAAUCACAUUUGAGGUGGUUAUGAAAAAAAUUGCAUGUCUUUCAGCACUGGCCGCAGUUCUGGCUUUCACCGCAGGUACUUCCGUAGCUGCGACUUCUACUGUAACUGGCGGUUACGCAC --mode=H
default mode
target
192 226
| |
5'-CUG...AUUU A AAAAAAAUU C ACUG...CAC-3'
GAGGUGGUU UG GCA UGU UUUCAGC
||||||||| || ||| ||| |||||||
CUCCACCAA AC CGU ACA AAAGUCG
3'-UUU...AUUC GG CAUGUCGAU AAAAUACCCAAU A -5'
| |
48 1
query
interaction energy = -14.2394 kcal/mol
helix-based prediction
target
192 226
| |
5'-CUG...AUUU A AAAAAAAUU C ACUG...CAC-3'
GAGGUGGUU UG GCAU GU UUUCAGC
||||||||| || |||| || |||||||
CUCCACCAA AC CGUA CA AAAGUCG
3'-UUU...AUUC GG CAUGUCGAU AAAUACCCAAUA A -5'
| |
48 1
query
interaction energy = -13.7394 kcal/mol
This can be solved by a special handling of one-sided bulges, for which we only have to consider the addition of non-maximal helices (shifting the last bp to the next helix).
thinking about it, this also applies to all other loops... to bypass this problem, we would have to screen all subhelix lengths of the helix to be added. would be ok...
ping @RickGelhausen : something we should think about for the journal version of the paper
mhh... can only be done easily for the canonical helices... otherwise we have to trace the base pairs of the current helix... not good...
the more I think of it, the less good the idea is, since we do only store the energy of the maximal helix and would have to recompute energy terms.
so the alternative is to introduce a "--noLP" into the standard predictor and be done with it.