Knot-Filter

This web-serivce allows the user to check whether a certain RNA secondary structure with pseudoknots belongs to one or several of various classes of structures which can be handled by leading structure prediction tools. The secondary structure has to be encoded as dot bracket string using different types of brackets (see below) to express crossing loops.

Structure:

Notes:

Input strings can denote pairs by paren types "()", "[]", "{}" and "Aa", ..., "Zz".
Unpaired bases can be given as ":", "." or "|".
Details on algorithm and classes can be found in "Markus Nebel, Frank Weinberg. Algebraic and Combinatorial Properties of Common RNA Pseudoknot Classes with Applications. Journal of Computational Biology (2012) 19(10): 1134-1150."