name: MC-Fold-DP
version: 0.1.0.1
author: Christian Hoener zu Siederdissen, Stephan H Bernhart, Peter F Stadler, Ivo L Hofacker
copyright: Christian Hoener zu Siederdissen, 2010-2011
homepage: http://www.tbi.univie.ac.at/software/mcfolddp/
maintainer: choener@tbi.univie.ac.at
category: Bioinformatics
license: GPL-3
license-file: LICENSE
build-type: Simple
stability: experimental
cabal-version: >= 1.4.0
synopsis:
Folding algorithm based on nucleotide cyclic motifs.
description:
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",
2011, submitted
.
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.
.
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:
.
* comparable prediction accuracy on sequences
.
* possibility to use sparse data correction
.
* handles non-ACGU nucleotides gracefully
.
* suboptimals: return all structures within an energy band above the ground state
.
* constraint folding (fill partial structures)
.
Todo:
.
* Boltzmann likelihood calculations
.
* pseudoknot calculations (currently aiming for a pknotsRG-like algorithm)
Flag fastBuild
description: build using fast GHC options (developer only!)
default: False
library
build-depends:
base >= 4 && < 5,
vector,
tuple,
PrimitiveArray,
Biobase == 0.3.1.1
exposed-modules:
BioInf.MCFoldDP
if flag(fastBuild)
ghc-options:
-O0
else
ghc-options:
-Odph
if impl(ghc > 6.13)
ghc-options:
-fllvm
executable MCFoldDP
build-depends:
cmdargs == 0.6.8,
split
main-is:
MCFoldDP.hs
if flag(fastBuild)
ghc-options:
-O0
else
ghc-options:
-Odph
if impl(ghc > 6.13)
ghc-options:
-fllvm