ViennaRNA / forgi

An RNA manipulation library.
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Are angle types the correct way to identify pseudoknots? #14

Closed Bernhard10 closed 5 years ago

Bernhard10 commented 8 years ago

Pseudoknots are identified by the connection_type, e.g. in is_node_pseudoknot. A connection type of 5 means pseudoknot.

However, every pseudoknot typically contains one multiloop segment of connection type 5, while the remaining segments are of type 2,3 or 4.

I don't think we can pinpoint the pseudoknot to this specific multiloop segment.

This might also influence the stats for not-pseudoknot loops of type 2-4

pseudoknots

Bernhard10 commented 5 years ago

This should be fixed in forgi 2.0