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. 2007 Aug 10;3(8):e149. doi: 10.1371/journal.pcbi.0030149

Figure 3. Sampling Alignment and Structure.

Figure 3

We sample a new alignment by choosing a random window of the alignment that is devoid of base-pairs and by realigning it (step 1). We then sample a new RNA structure by removing a random set of helices from the given structure (step 2) and by adding a set of new helices (step 3).