Author: Theis, Corinna; Reeder, Jens; Giegerich, Robert
Title: KnotInFrame: prediction of -1 ribosomal frameshift events Document date: 2008_9_27
ID: 4ov0j2u3_26
Snippet: Filtering of unlikely foldings. Subsequent filtering is based on the candidates' energy values. The low energy filter (LEF) discards candidates x ¼ pu where pknotsRG-fs(u) > . We choose the threshold a = À7.4 kcal/mol, since all pseudoknots in our test set achieve this or a lower energy value. Next, the energy difference filter (EDF) discards candidates that rather fold into an unknotted structure, i.e. RNAfoldðuÞ þ < pknotsRG-fsðuÞ. The d.....
Document: Filtering of unlikely foldings. Subsequent filtering is based on the candidates' energy values. The low energy filter (LEF) discards candidates x ¼ pu where pknotsRG-fs(u) > . We choose the threshold a = À7.4 kcal/mol, since all pseudoknots in our test set achieve this or a lower energy value. Next, the energy difference filter (EDF) discards candidates that rather fold into an unknotted structure, i.e. RNAfoldðuÞ þ < pknotsRG-fsðuÞ. The default value for the parameter is 8.7 kcal/mol, also derived from RECODE analysis.
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