Many more alternatives to these kinematic structures can also be obtained by altering the location and the type of driving joints within loops or by changing some partial sub-structures relevant to the branch loops.
For each of the stages, input branches, loop filters, and feedback branches were modeled as potential mismatch sources.
Both the A4C mutation and the original structure contain a multi-branch loop, while our reported mutation's structure does not.
For example, two RNA structures with four stems can be considerably different if the first structure is arranged as a one elongated structure containing a bulge and three consecutive loops, while the second includes a bulge, a multi-branch loop, and two additional stem-loops that branch out of the multi-branch loop.
However, free energy evaluation of a given sequence/structure pair, as done by RNAeval, may introduce these extra cases in the near future as an additional parameter, such as logarithmic multi-branch loop evaluation.
Each siRNA sequence was manually aligned to the correspondent global mRNA secondary structure to discriminate the local targeted site among loop, 5′-loop, 3′-loop, internal loop (int-loop), multi-branch loop (mb-loop), H-loop, bulge loop (b-loop), one base bulge (one-bb) and stem structures.
As in secondary structure folding, the loop type is determined by E R [ i, j ]≔ E R as follows: E R = ∅, hairpin loop; E R = E i R and | E R | = 1, interior loop (including bulge and stacks); E R = E i R, | E R |≥2, multi-branch loop; E R = E e R, kissing-hairpin loop; | E i R |, | E e R | ≥ 1, general kissing loop.
And in the frail December light there were glimpses of subtle beauty: the dark bare Japanese-print branches looped and netted, snowflakes glittering like jewels in the windy air and in the distance the gray towers of Manhattan brooding like chessmen.
This grammar (and all the derivatives that we tested) are capable of modeling the salient features of ncRNA secondary structure (including hairpins, bulges, interior loops, and multi-branch loops).
In particular, several additional energy parameters for the different loop types (hairpin loops, interior loops and multi-branch loops) were introduced.
