“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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The tool - STRMS<br />
(Structural RNA Motif Search):<br />
� Input: Secondary <strong>structure</strong> of the query, <strong>in</strong>clud<strong>in</strong>g local sequence<br />
and <strong>structure</strong> constra<strong>in</strong>ts, and a target sequence database.<br />
� Output: All occurrences of the query <strong>in</strong> the target, ranked by their<br />
similarity to the query [<strong>in</strong> html file].<br />
� The tool is <strong>flexible</strong> and takes <strong>in</strong>to account a large number of<br />
sequence options.<br />
� Our approach comb<strong>in</strong>es:<br />
� pre-fold<strong>in</strong>g with MFOLD (Zuker, 2003)<br />
� RNA pattern match<strong>in</strong>g algorithm [O(mn)] <strong>based</strong> on subtree<br />
homeomorphism <strong>for</strong> ordered, rooted trees.
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