The BiobaseFR3D package
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
Properties
| Versions | 0.1.0.1, 0.1.1.0, 0.1.3.0, 0.2.2.0, 0.2.3.0 |
|---|---|
| Dependencies | base (>3 & <5), BiobaseXNA (0.6.2.0), bytestring, containers, filemanip, iteratee, tuple |
| License | GPL-3 |
| Copyright | Christian Hoener zu Siederdissen, 2011 |
| Author | Christian Hoener zu Siederdissen |
| Maintainer | choener@tbi.univie.ac.at |
| Stability | experimental |
| Category | Bioinformatics |
| Home page | http://www.tbi.univie.ac.at/~choener/ |
| Upload date | Thu Feb 16 14:20:59 UTC 2012 |
| Uploaded by | ChristianHoener |
| Built on | ghc-7.4 |
Modules
Downloads
- BiobaseFR3D-0.2.3.0.tar.gz (Cabal source package)
- package description (included in the package)