Software Listing of Author : "Bibiserv"

Locomotif: Localization of RNA motifs with generated thermodynamic Matchers

Locomotif is a GUI-based program that allows for the visual design of RNA motifs. The graphical structures are then translated into executable programs to be used for searching a motif in a sequence (plain text or FASTA format).

  • Platform: WinOther

pknotsRG is a tool for folding RNA secondary structures, including the class of simple recursive pseudoknots. The program runs in O(n^4) time and O(n^2) space, therefore its application here on the BiBiserv is limited to sequences of length up to 800 bases. The energy parameters for structures containing no pseudoknots are the same as in the actual mfold 3.1. The energy for pseudoknots is computed with a model similar to that used by Rivas&Eddy in pknots. The folding temperature is fixed to 37C.
Currently, there are three different modes available:

pknotsRG-mfe: computes the structure of s (knotted or not) of minimal free energy.
pknotsRG-enf: enforces a pseudoknot: it delivers the energetically best complete structure of s that includes at least one pseudoknot somewhere.
pknotsRG-loc: delivers the best...

  • Platform: WinOther

RNAMovies is a system for the visualization of RNA secondary structure spaces, i.e. multiple sets of secondary structure data. The program creates an interpolated animation of the data using the well-known NAVIEW-routines. The highlighting of pseudo-knotted regions is also supported.
This page relates to the new Java version of RNA Movies that replaces the former online-version as well as the standalone-versions.
The new version features SVG-export for high quality graphics as well as several image formats(JPEG,PNG and GIF). Single or multiple image export is supported. Additionally to its own formats RNAMovies supports DSCE and RNAStructML as input format

  • Platform: WinOther
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