Predicts all PLM model pseudoknots within an RNA sequence in a neighboring-region-interference-free fashion. The PLM model is derived from the existing Pseudobase entries. The innovative DPSS approach calculates the optimally lowest stacking energy between two partner sequences. Combined with the Mfold, PLMM_DPSS can also be used in predicting complicated pseudoknots.
Pseudoknot Local Motif Model and Dynamic Partner Sequence Stacking
Web user interface
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Department of Pathology and Microbiology, University of Nebraska Medical Center Omaha, NE, USA; Department of Computer Science, College of Information Science and Technology, University of Nebraska at Omaha Omaha, NE, USA