Biomedical Engineering Reference
In-Depth Information
Take sole unfolded
fragment
R start,end := R 1 ,n
Take one of the
unfolded fragments
R start,end
Still exist
unfolded
fragments?
no
Start
End
yes
Start folding of
R start,end
Recursively fold
new (paired)
substructure
S ii,jj on
R start,end
(Further)
hairpin
possible on
R start,end ?
Finish folding of
R start,end
(unfolded positions
become unpaired)
no
yes
Sample hairpin loop
S ii,jj on R start,end
S ii,jj
extendable
on
R start,end ?
no
Finish folding of
substructure S ii,jj
yes
Sample extension of
S ii,jj on R start,end
Substructure of
exterior loop :
S ii,jj is extended by
adding a preceding
single-strand of
arbitrary length
Stacking :
S ii,jj is extended by
adding enclosing base
pair(s)
Extension
type
Update ii and jj
Bulge or interior :
S ii,jj is extended by
adding a preceding or
a following
single-strand (or both)
Substructure of
multiple loop :
S ii,jj is extended by
adding a preceding
single-strand of
arbitrary length
Update end
(must be indeed the
last position of the
multiloop)
Update start
(not necessarily the
first position of the
multiloop)
no
substructure of exterior loop
Recursively fold
new (paired)
substructure
S ii,jj on
R start,end
Multiloop
complete?
Structure
type
yes
substructure of multiple loop
Fig. 5. Flowchart for recursive sampling of an RNA secondary structure S 1 ,n for a given input
sequence r of length n according to a less restrictive strategy with extensively more freedom (that
requires dynamic validation of possible random choices during the sampling process)
considered fragment R start,end . Figure 5 gives a schematic overview on this inside-out
fashion sampling strategy; a simple example is presented in Fig. 6.
Note that in order to ensure that all sampled substructures can be successfully folded,
especially in the case of multiloops, we have to take care that at any point, the strategy
may only draw such random choices that do not make it impossible to successfully fin-
ish the currently running construction process (of a particular loop). As this strongly
depends on the actual positions and types of all previously folded paired substructures,
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