Author: Reeder, Jens; Steffen, Peter; Giegerich, Robert
Title: pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows Document date: 2007_5_3
ID: zgv4kd6j_11
Snippet: (i) MFE structure only: The computed secondary structure and its energy are displayed in Vienna (Dot-Bracket) Notation. Here, a pair of opening and closing parenthesis denotes a base pair, a dot represents a single stranded nucleotide. A 2D visualization is generated using the PseudoViewer Web service (10) . Also, a link to a Connect formatted file, originally used by Michael Zukers mfold (11), is provided. An example output is shown in Figure 1 .....
Document: (i) MFE structure only: The computed secondary structure and its energy are displayed in Vienna (Dot-Bracket) Notation. Here, a pair of opening and closing parenthesis denotes a base pair, a dot represents a single stranded nucleotide. A 2D visualization is generated using the PseudoViewer Web service (10) . Also, a link to a Connect formatted file, originally used by Michael Zukers mfold (11), is provided. An example output is shown in Figure 1 . (ii) Suboptimal solutions: The list of suboptimal solutions is displayed as an RNAmovie (12). RNAmovies displays the individual suboptimal structures one after another with an adjustable number of intermediate transition steps. This allows for a smooth morphing from one structure to the next. Additionally, all suboptimal structures are displayed as Vienna strings along with their respective energy value at the bottom of the result page. (iii) Window mode: For each window, the start and end position is displayed, followed by the result of the window folding. This may be one structure (as Vienna string), or many if the suboptimal mode is also selected. There is currently no vizualization provided, when using the window mode. However, the user can resubmit the sequence of an interesting window on its own. Then, the vizualizations explained in (i) and (ii) are automatically generated.
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