1 2The wuss module implements routines for using WUSS notation to 3represent RNA secondary structures. 4 5The API provides the following converters: 6 7\begin{tabular}{ll} 8\ccode{esl\_wuss2ct()} & Convert WUSS string to Zuker CT array. \\ 9\ccode{esl\_ct2wuss()} & Convert CT array (no pk's) to WUSS string. \\ 10\ccode{esl\_wuss2kh()} & Convert WUSS string to old format (Konings/Hogeweg).\\ 11\ccode{esl\_kh2wuss()} & Convert old format to WUSS string.\\ 12\ccode{esl\_wuss\_full()}& Convert simple WUSS to full (output) WUSS.\\ 13\ccode{esl\_wuss\_nopseudo()} & Crudely remove pseudoknot annotation from WUSS string.\\ 14\end{tabular} 15 16WUSS notation is defined later in the Formats section of this 17document. 18 19So-called ``old'' (KH) format (old because COVE used it, whereas 20Infernal uses WUSS) for a secondary structure annotation string used 21\ccode{><} pairs to annotate base pairs, as in \ccode{>>>....<<<} for 22a three-base stem with a four-base single stranded loop. 23 24A CT array is a \ccode{1..n} array for a sequence of length \ccode{n}, 25where \ccode{ct[i]} is either an index \ccode {1..n} of a position 26that residue \ccode{i} base pairs to, or 0 if \ccode{i} is unpaired. 27 28 29 30 31 32 33 34 35