The MC-Fold-DP package

[Tags: gpl, library, program]

This is a RNA secondary structure prediction tool based on the idea of combining small motifs, called nucleotide cyclic motifs (NCMs). The algorithm implemented here and 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/

has polynomial runtime in O(n^3) and uses a (pseudo-energy) scoring scheme based on

Parisien M, Major F.

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data,

Nature 2008, 452(7183):51-55. http://www.major.iric.ca/MC-Fold/

This program uses the same database as MC-Fold (which has exponential run-time) and aims to be able to produce the same results.

The underlying grammar of our implementation is unambiguous and allows the complete evaluation of all structures within an energy band above the ground state, presenting each unique structure just once. Alternatively, the grammar allows partition function calculations.

Current status:

Todo:


Properties

Versions0.1.0.0, 0.1.0.1, 0.1.1.0
Dependenciesbase (==4.*), Biobase (==0.3.1.1), cmdargs (==0.10.*), PrimitiveArray, split, tuple, vector
LicenseGPL-3
CopyrightChristian Hoener zu Siederdissen, 2010-2011
AuthorChristian Hoener zu Siederdissen, Stephan H Bernhart, Peter F Stadler, Ivo L Hofacker
Maintainerchoener@tbi.univie.ac.at
Stabilityexperimental
CategoryBioinformatics
Home pagehttp://www.tbi.univie.ac.at/software/mcfolddp/
ExecutablesMCFoldDP
UploadedMon Nov 12 21:42:13 UTC 2012 by ChristianHoener
Downloads394 total (18 in last 30 days)
StatusDocs uploaded by user
Build status unknown [no reports yet]

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