“A structure based flexible search method for motifs in RNA” Isana ...
“A structure based flexible search method for motifs in RNA” Isana ...
“A structure based flexible search method for motifs in RNA” Isana ...
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Deal<strong>in</strong>g with Potential Pseudoknots<br />
Observations:<br />
� These edges break down the tree-like<br />
representation of the RNA secondary <strong>structure</strong>s.<br />
� The potential pseudoknot is conf<strong>in</strong>ed to the<br />
subtree rooted <strong>in</strong> node 8, i.e., node 2 and node 4<br />
are sibl<strong>in</strong>g nodes shar<strong>in</strong>g a common parent node.<br />
� For all riboswitch aptamer queries <strong>in</strong> this study,<br />
only one potential pseudoknot is predicted and it<br />
is always <strong>for</strong>med between two sibl<strong>in</strong>g leaf nodes<br />
shar<strong>in</strong>g a common parent node.<br />
� The text subtrees could be annotated with any<br />
number of potential sibl<strong>in</strong>g pseudoknots*.<br />
* <strong>based</strong> on loop sequence complementarity analysis that is executed <strong>in</strong> the preprocess<strong>in</strong>g stage.<br />
sibl<strong>in</strong>g pseudoknot edge
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