The RNAwolf package

[ Tags: bioinformatics, gpl, library, program ] [ Propose Tags ]

The algorithm implemented here-in provides extended RNA secondary structure prediction. Each predicted nucleotide pairing is extended with an annotation describing which of three nucleotide edges is engaged in the pairing. In addition, each nucleotide may be engaged in more than one pairing.

The algorithm is described in

Hoener zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL,

"A Folding Algorithm for Extended RNA Secondary Structures",

Bioinformatics (2011) 27 (13), i129-136

http://www.tbi.univie.ac.at/software/rnawolf/

Please note that "experimental" does mean experimental. We are mostly concerned with determining a good set of (heuristic) rules for run-time reduction currently. This version does include stacking and is able to fold sequences of a few hundred nucleotides in seconds.

Triplet calculations will come back with the next version (in a few days). The recursions require a number of changes to keep the runtimes down (as has been done for the extended loops without triplets).

We have recently split the Biohaskell libraries into smaller individual libraries. In addition, stacking, intermediate arrays, fusion and newtype-wrapping did require a number of changes. Please send a mail, if you encounter strange behaviour or bugs.

Changes in 0.4.0.0

Changes in 0.3.2.0

Changes in 0.3.1.0

Properties

Versions 0.3.0.0, 0.3.0.1, 0.3.0.2, 0.3.1.0, 0.3.2.0, 0.4.0.0
Dependencies base (==4.*), BiobaseTrainingData (>=0.1.2.3), BiobaseXNA, bytestring, cmdargs (==0.8.*), containers, deepseq, directory, parallel, PrimitiveArray, random, split, StatisticalMethods, vector [details]
License GPL-3
Copyright Christian Hoener zu Siederdissen, 2010-2011
Author Christian Hoener zu Siederdissen, Stephan H Bernhart, Peter F Stadler, Ivo L Hofacker
Maintainer choener@tbi.univie.ac.at
Category Bioinformatics
Home page http://www.tbi.univie.ac.at/software/rnawolf/
Uploaded Thu Sep 29 14:47:37 UTC 2011 by ChristianHoener
Distributions NixOS:0.4.0.0
Executables RNAwolf, RNAwolfTrain
Downloads 1812 total (17 in the last 30 days)
Rating 0.0 (0 ratings) [clear rating]
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Status Docs uploaded by user
Build status unknown [no reports yet]
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