Users and friends of pknotsRG. The online service of pknotsRG will be discontinued in near future. The latest version of pKiss includes the same functionality within a modern web application. Consider using pKiss for your task.

Users and friends of pknotsRG. The online service of pknotsRG will be discontinued in near future. The latest version of pKiss includes the same functionality within a modern web application. Consider using pKiss for your task.

• The maximal sequence length is set to 800 bases.
• All non-nucleotide characters (i.e. not A,C,G,T,U,N) are removed from the sequence. The nucleotide T is treated as U.
• Input can be in upper or lower case, even mixed.
• N characters are allowed but are unpaired and undangled in all computed secondary structures.
• Choosing a maximal size for pseudoknots improves the runtime drastically. Furthermore the results may become more meaningful, since the current energy model doesn't seem to fit very well for very large pseudoknots (>200 bases).
• In suboptimal mode only the first one hundred structures are displayed. These may not be the best one hundred, since the order depends on the backtracking recurrencies. Use the Set button for an automatic guess of a good value (only works when sequence is pasted into text field). If this value turns out to be inappropriate, i.e. far less than 100 structures are reported, return to this page and slightly increase the energy difference value. However, the maximal value is 10 kcal/mol.
• The window mode is activated once you specify a window size. The default increment is 1, unless another value is provided. At the moment we display only the raw program output. If you need the graphics of an individual folding, resubmit the corresponding window's sequence alone without the window mode selected.