The MC-Fold-DP package

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

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

Versions 0.1.0.0, 0.1.0.1, 0.1.1.0
Dependencies base (==4.*), Biobase (==0.3.1.1), cmdargs (==0.10.*), PrimitiveArray, split, tuple, 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/mcfolddp/
Uploaded Mon Nov 12 21:42:13 UTC 2012 by ChristianHoener
Distributions NixOS:0.1.1.0
Executables MCFoldDP
Downloads 1002 total (21 in the last 30 days)
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