Selected article for: "FASTA format and input format"
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_10
    Snippet: The pknotsRG Web Server (http://bibiserv.techfak.unibielefeld.de/pknotsrg) offers an easy and comfortable way to use the pknotsRG algorithm. Input has to be provided in a FASTA format containing one single RNA sequence. All non-nucleotide characters (i.e not A,C,G,T,U,N in upper or lower case) are removed from the sequence. The nucleotide 'T' is treated as 'U' during the folding routine, 'N's are always unpaired. The user selects one of the three.....
    Document: The pknotsRG Web Server (http://bibiserv.techfak.unibielefeld.de/pknotsrg) offers an easy and comfortable way to use the pknotsRG algorithm. Input has to be provided in a FASTA format containing one single RNA sequence. All non-nucleotide characters (i.e not A,C,G,T,U,N in upper or lower case) are removed from the sequence. The nucleotide 'T' is treated as 'U' during the folding routine, 'N's are always unpaired. The user selects one of the three basic modes and optionally an energy threshold for suboptimal enumeration. If he wants to use the window mode, at least the window size has to be specified. The default window increment is set to one, unless otherwise specified. Depending on the user selection, there are three different ways how the result is displayed:

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