BiobaseFR3D

Importer for FR3D resources http://www.tbi.univie.ac.at/~choener/

Latest on Hackage:0.2.3.0

This package is not currently in any snapshots. If you're interested in using it, we recommend adding it to Stackage Nightly. Doing so will make builds more reliable, and allow stackage.org to host generated Haddocks.

GPL-3 licensed by Christian Hoener zu Siederdissen

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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