BiobaseFR3D: Importer for FR3D resources

[ bioinformatics, gpl, library ] [ Propose Tags ]

Provides importers for FR3D resource files. Of particular interest are basepairs files which describe canonical and non-canonical (non-Watson-Crick) base pairings in RNA secondary structure.

The original FR3D paper is:

FR3D: Finding Local and Composite Recurrent Structural Motifs in RNA 3D Structures, Michael Sarver; Craig L. Zirbel; Jesse Stombaugh; Ali Mokdad; Neocles B. Leontis. /Journal of Mathematical Biology/ (2008) 56:215–252.

Changes since any 0.1.*:

  • Zero-based indexing (FR3D is one-based!) for sequence positions. We do not change the nucleotide PDB number.

  • Some sanity checks, a number of FR3D files fall through at this and need to be checked for consistency


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Dependencies base (>3 && <5), BiobaseXNA (==, bytestring, containers, filemanip, iteratee, tuple [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, 2011
Author Christian Hoener zu Siederdissen
Category Bioinformatics
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Uploaded by ChristianHoener at 2012-02-16T14:20:59Z
Reverse Dependencies 2 direct, 1 indirect [details]
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