name:           MC-Fold-DP
version:        0.1.1.0
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:  >= 1.6.0
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",
                .
                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:
                .
                * comparable prediction accuracy on sequences (compared with MC-Fold)
                .
                * 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:
      -O2

executable MCFoldDP
  build-depends:
    cmdargs == 0.10.* ,
    split
  main-is:
    MCFoldDP.hs
  if flag(fastBuild)
    ghc-options:
      -O0
  else
    ghc-options:
      -O2