RNAdesign 0.1.1.0 → 0.1.2.1
raw patch · 4 files changed
+34/−14 lines, 4 filesdep ~ViennaRNA-bindings
Dependency ranges changed: ViennaRNA-bindings
Files
- BioInf/RNAdesign.hs +5/−3
- README.md +6/−0
- RNAdesign.cabal +19/−11
- changelog +4/−0
BioInf/RNAdesign.hs view
@@ -60,8 +60,10 @@ resolveOpt :: String -> t -> Primary -> [D1Secondary] -> Double resolveOpt optfun ener inp secs = parseOptString l sops mops gops props optfun where l = length secs+ i = concatMap show $ VU.toList inp sops =- [ ("eos" , \k -> unsafePerformIO $ RNA.eos (concatMap show (VU.toList inp)) (fromD1S $ secs !! (k-1)))+ [ ("eos" , \k -> unsafePerformIO $ RNA.eos i (fromD1S $ secs !! (k-1)))+ , ("partc" , \k -> sel1 . unsafePerformIO $ RNA.partConstrained i (fromD1S $ secs !! (k-1))) , ("ed" , \k -> ensembleDefect inp (secs !! (k-1))) -- ensemble defect ] mops =@@ -71,8 +73,8 @@ ] gops = [ ("Ged" , probabilityDefectAll inp secs) -- global ensemble defect a la ``me''- , ("gibbs" , sel1 . unsafePerformIO $ RNA.part (concatMap show (VU.toList inp)))- , ("mfe" , fst . unsafePerformIO $ RNA.mfe (concatMap show (VU.toList inp)))+ , ("gibbs" , sel1 . unsafePerformIO $ RNA.part i)+ , ("mfe" , fst . unsafePerformIO $ RNA.mfe i) ] props = [ ("logMN", \ps -> lmn ps inp)
README.md view
@@ -77,6 +77,12 @@ eos :: energy of a structure: eos(1) ed :: ensemble defect of a structure: ed(3)+partc :: constrained partition function: partc(1).++You probably want to use partc in conjunction with eos, where eos is modified+by a small constant: "0.1 * eos(1) + partc(1)". eos guides the optimizer to the+first viable sequence, after which the constrained partition function becomes+active. ### nullary, constant for the current sequence:
RNAdesign.cabal view
@@ -1,7 +1,7 @@ name: RNAdesign-version: 0.1.1.0-author: Christian Hoener zu Siederdissen, 2013-2014-copyright: Christian Hoener zu Siederdissen, Stefan Hammer, Ingrid Abfalter, Ivo L. Hofacker, Christoph Flamm, Peter F. Stadler, 2013-2014+version: 0.1.2.1+author: Christian Hoener zu Siederdissen+copyright: Christian Hoener zu Siederdissen, 2013-2014 maintainer: choener@tbi.univie.ac.at category: Bioinformatics synopsis: Multi-target RNA sequence design@@ -12,27 +12,35 @@ cabal-version: >= 1.6.0 description: The RNA sequence design problem asks for a single sequence that- readily folds into the one or more structural targets that are- given as input.+ readily folds into the (one or more) structural targets that+ are given as input. . This program expects on standard input a file with one or more- structures and, possibly, additional sequence constraints. It- will then run a Markov chain to find a sequence that is optimal- with regard to the structural targets and the user-defineable- optimization function.+ structures and, possibly, additional sequence constraints in+ the form of an IUPAC string. It will then run a Markov chain to+ find a sequence that is optimal with regard to the structural+ targets and the user-defineable optimization function. . The user can give different optimization criteria on the command line, akin to a simple calculator. .+ For more details please consult:+ <https://github.com/choener/RNAdesign/blob/master/README.md> .+ You can also run @RNAdesign --showmanual@ which will display+ the same @README.md@. .+ .+ . If you find this program useful, please cite: . @ Christian Hoener zu Siederdissen, Stefan Hammer, Ingrid Abfalter, Ivo L. Hofacker, Christoph Flamm, Peter F. Stadler Computational design of RNAs with complex energy landscapes- 2013. Biopolymers. 99, no. 12. 99. 1124–36. http://dx.doi.org/10.1002/bip.22337+ 2013. Biopolymers. 99, no. 12. 99. 1124–36. @+ .+ <http://dx.doi.org/10.1002/bip.22337> @@ -63,7 +71,7 @@ ParsecTools >= 0.0.2 && < 0.0.3 , PrimitiveArray >= 0.5.3 , RNAFold >= 1.99.3.3 ,- ViennaRNA-bindings >= 0.1.0.0+ ViennaRNA-bindings >= 0.1.1.1 exposed-modules: BioInf.RNAdesign BioInf.RNAdesign.Assignment
changelog view
@@ -1,3 +1,7 @@+0.1.2.1++- constrained partition function enabled+ 0.1.1.0 - IUPAC nomenclature for sequence constraints