diff --git a/Biobase/Vienna.hs b/Biobase/Vienna.hs --- a/Biobase/Vienna.hs +++ b/Biobase/Vienna.hs @@ -1,6 +1,8 @@ {-# LANGUAGE NoMonomorphismRestriction #-} -- | Turner energy data as used in the ViennaRNA package. +-- +-- TODO should use energy type for tables, not int! module Biobase.Vienna where @@ -9,6 +11,8 @@ import Data.Ix.Tuple import Data.PrimitiveArray.Ix import Data.PrimitiveArray +import Biobase.Types.Partition +import Biobase.Types.Energy import Biobase.RNA import Biobase.Turner.Tables @@ -18,8 +22,12 @@ -- Type for Vienna Tables -type ViennaEnergySet = (Temperature, ViennaTables, ViennaTables) -type ViennaTables = Turner2004 ViennaPair Nucleotide Int +-- type ViennaEnergySet = (Temperature, ViennaTables, ViennaTables) + +type ViennaIntTables = Turner2004 ViennaPair Nucleotide Int +type ViennaEnergyTables = Turner2004 ViennaPair Nucleotide Energy +type ViennaPartitionTables = Turner2004 ViennaPair Nucleotide Partition + type Temperature = Double @@ -28,7 +36,7 @@ -- are commented out. Activate them in BiobaseTurner before doing the same -- here! -emptyTables :: ViennaTables +emptyTables :: ViennaIntTables emptyTables = Turner2004 --stack { stack = emptyIV diff --git a/Biobase/Vienna/Default.hs b/Biobase/Vienna/Default.hs --- a/Biobase/Vienna/Default.hs +++ b/Biobase/Vienna/Default.hs @@ -14,7 +14,7 @@ import Biobase.Vienna.Import.ViennaPar import Biobase.Turner.Tables import Biobase.Vienna - +import Biobase.Types.Energy @@ -23,4 +23,5 @@ -- Turner entropy and enthalpy tables. -turner2004GH = importPar $ B.unpack defaultPars +turner2004GH = (dmap Energy ta,dmap Energy tb) where + (ta,tb) = importPar $ B.unpack defaultPars diff --git a/Biobase/Vienna/Export/ViennaC.hs b/Biobase/Vienna/Export/ViennaC.hs new file mode 100644 --- /dev/null +++ b/Biobase/Vienna/Export/ViennaC.hs @@ -0,0 +1,264 @@ +{-# LANGUAGE ScopedTypeVariables #-} +{-# LANGUAGE TemplateHaskell #-} + +-- | Exports the Vienna energy tables as a number of C files (one .c file, a +-- number .h files). For this reason, files are written into a target +-- directory! + +module Biobase.Vienna.Export.ViennaC + ( export + ) where + +import Prelude hiding (pi) +import Text.Printf +import System.Directory +import Data.List.Split +import Data.List +import qualified Data.Map as M +import Data.FileEmbed +import qualified Data.ByteString.Char8 as B + +import Biobase.Turner.Tables +import Biobase.Vienna +import Data.PrimitiveArray +import Biobase.RNA + +import Biobase.Vienna.Default + +(g,h) = turner2004GH + + + +type Directory = FilePath + +-- | Export the files required for default values in the ViennaRNA 2.0 C +-- package. + +export :: ViennaIntTables -> ViennaIntTables -> Directory -> IO () +export trnrG trnrH target = mapM_ (\f -> f trnrG trnrH target) [exportC, export11, export21, export22] + + + +-- | Export the main C file + +exportC :: ViennaIntTables -> ViennaIntTables -> Directory -> IO () +exportC trnrG trnrH target = writeFile (target ++ "/energy_par.c") out where + out = unlines [ B.unpack $(embedFile "templates/cheader") , xs, stck, lps, mms, dngls, tris, tets, hexs,includes] + xs = unlines + [ pd "lxc37" $ largeLoop trnrG + , pi "ML_intern37" $ multiHelix trnrG + , pi "ML_interndH" $ multiHelix trnrH + , pi "ML_closing37" $ multiOffset trnrG + , pi "ML_closingdH" $ multiOffset trnrH + , pi "ML_BASE37" $ multiNuc trnrG + , pi "ML_BASEdH" $ multiNuc trnrH + , pi "MAX_NINIO" $ maxNinio trnrG + , pi "ninio37" $ ninio trnrG + , pi "niniodH" $ ninio trnrH + , pi "TerminalAU37" $ termAU trnrG + , pi "TerminalAUdH" $ termAU trnrH + , pi "DuplexInit37" $ intermolecularInit trnrG + , pi "DuplexInitdH" $ intermolecularInit trnrH + , pi "TripleC37" 100 + , pi "TripleCdH" 1860 + , pi "MultipleCA37" 30 + , pi "MultipleCAdH" 340 + , pi "MultipleCB37" 160 + , pi "MultipleCBdH" 760 + ] + stck = unlines + [ "PUBLIC int stack37[NBPAIRS+1][NBPAIRS+1] =" + , (block2 8 . toList $ stack trnrG) + , "PUBLIC int stackdH[NBPAIRS+1][NBPAIRS+1] =" + , (block2 8 . toList $ stack trnrH) + ] + lps = unlines + [ "PUBLIC int hairpin37[31] = {" ++ (concat . intersperse "," . map printNum . toList $ hairpinL trnrG) ++ "};" + , "PUBLIC int hairpindH[31] = {" ++ (concat . intersperse "," . map printNum . toList $ hairpinL trnrH) ++ "};" + , "PUBLIC int bulge37[31] = {" ++ (concat . intersperse "," . map printNum . toList $ bulgeL trnrG) ++ "};" + , "PUBLIC int bulgedH[31] = {" ++ (concat . intersperse "," . map printNum . toList $ bulgeL trnrH) ++ "};" + , "PUBLIC int internal_loop37[31] = {" ++ (concat . intersperse "," . map printNum . toList $ iloopL trnrG) ++ "};" + , "PUBLIC int internal_loopdH[31] = {" ++ (concat . intersperse "," . map printNum . toList $ iloopL trnrH) ++ "};" + ] + mms = unlines + [ writeMM "I" iloopMM trnrG trnrH + , writeMM "H" hairpinMM trnrG trnrH + , writeMM "M" multiMM trnrG trnrH + , writeMM "1nI" iloop1xnMM trnrG trnrH + , writeMM "23I" iloop2x3MM trnrG trnrH + , writeMM "Ext" extMM trnrG trnrH + ] + dngls = unlines + [ "PUBLIC int dangle3_37[NBPAIRS+1][5] =" + , block2 5 . toList $ dangle3 trnrG + , "PUBLIC int dangle3_dH[NBPAIRS+1][5] =" + , block2 5 . toList $ dangle3 trnrH + , "PUBLIC int dangle5_37[NBPAIRS+1][5] =" + , block2 5 . toList $ dangle5 trnrG + , "PUBLIC int dangle5_dH[NBPAIRS+1][5] =" + , block2 5 . toList $ dangle5 trnrH + ] + t3 = getLookup 3 trnrG trnrH + t4 = getLookup 4 trnrG trnrH + t6 = getLookup 6 trnrG trnrH + tris = writeTabbed 3 "Triloop" t3 + tets = writeTabbed 4 "Tetraloop" t4 + hexs = writeTabbed 6 "Hexaloop" t6 + + includes = unlines $ map ((++ "\"") . ("#include \""++)) + [ "intl11.h" + , "intl11dH.h" + , "intl21.h" + , "intl21dH.h" + , "intl22.h" + , "intl22dH.h" + ] + + + +-- | Export iloops 1x1 + +export11 :: ViennaIntTables -> ViennaIntTables -> Directory -> IO () +export11 trnrG trnrH target = writeFile (target ++ "/intl11.h") outG >> writeFile (target ++ "/intl11dH.h") outH where + outG = unlines + [ "PUBLIC int int11_37[NBPAIRS+1][NBPAIRS+1][5][5] =" + , (block4 8 5 5 . toList $ iloop1x1 trnrG) + ] + outH = unlines + [ "PUBLIC int int11_dH[NBPAIRS+1][NBPAIRS+1][5][5] =" + , (block4 8 5 5 . toList $ iloop1x1 trnrH) + ] + + + +-- | Export iloops 2x1 + +export21 :: ViennaIntTables -> ViennaIntTables -> Directory -> IO () +export21 trnrG trnrH target = writeFile (target ++ "/intl21.h") outG >> writeFile (target ++ "/intl21dH.h") outH where + outG = unlines + [ "PUBLIC int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5] =" + , (block5 8 5 5 5 . toList $ iloop1x2 trnrG) + ] + outH = unlines + [ "PUBLIC int int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5] =" + , (block5 8 5 5 5 . toList $ iloop1x2 trnrH) + ] + + + +-- | Export iloops 2x2 + +export22 :: ViennaIntTables -> ViennaIntTables -> Directory -> IO () +export22 trnrG trnrH target = writeFile (target ++ "/intl22.h") outG >> writeFile (target ++ "/intl22dH.h") outH where + outG = unlines + [ "PUBLIC int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5] =" + , (block6 8 5 5 5 5 . toList $ iloop2x2 trnrG) + ] + outH = unlines + [ "PUBLIC int int22_dH[NBPAIRS+1][NBPAIRS+1][5][5][5][5] =" + , (block6 8 5 5 5 5 . toList $ iloop2x2 trnrH) + ] + + + +-- * Helper functions + +writeTabbed (ksize :: Int) key (ns,gs,hs) = unlines + [ printf "PUBLIC char %ss[%d] =" key ((ksize+3)*40+1) + , ns + , ";" + ] ++ printf "PUBLIC int %s37[40] = " key ++ gs ++ ";\n" + ++ printf "PUBLIC int %sdH[40] = " key ++ hs ++ ";\n" + +getLookup k trnrG trnrH = (nsF,gs,hs) where + nsF = concat $ intersperse "\n" $ map ((++ " \"") . (" \"" ++) . map nucleotideToChar) ns + ns = filter ((==(k+2)) . length) . M.keys $ hairpinLookup trnrG + gs = lkup trnrG + hs = lkup trnrH + lkup tbl = ("{"++) . (++"}") . concat . intersperse "," $ map (printNum . (hairpinLookup tbl M.!)) ns + +writeMM typ fun trnrG trnrH = unlines + [ printf "PUBLIC int mismatch%s37[NBPAIRS+1][5][5] =" typ + , block3 5 5 . toList $ fun trnrG + , printf "PUBLIC int mismatch%sdH[NBPAIRS+1][5][5] =" typ + , block3 5 5 . toList $ fun trnrH + ] + +block2 s2 xs + = (++ "};") + . ("{" ++) + . concat + . intersperse "\n," + . map ((++ "}") . ("{" ++) . concat . intersperse ",") + . splitEvery s2 + $ map printNum xs + +block3 s2 s3 xs + = (++ "};") + . ("{" ++) + . concat + . intersperse "\n," + . map ((++ "}") . ("{" ++) . concat . intersperse ",") + . splitEvery s2 + . map ((++ "}\n ") . ("{" ++) . concat . intersperse ",") + . splitEvery s3 + $ map printNum xs + +block4 s2 s3 s4 xs + = (++ "};") + . ("{" ++) + . concat + . intersperse "\n," + . map ((++ "}") . ("{" ++) . concat . intersperse ",") + . splitEvery s2 + . map ((++ "}\n ") . ("{" ++) . concat . intersperse ",") + . splitEvery s3 + . map ((++ "}\n ") . ("{" ++) . concat . intersperse ",") + . splitEvery s4 + $ map printNum xs + +block5 s2 s3 s4 s5 xs + = (++ "};") + . ("{" ++) + . concat + . intersperse "\n," + . map ((++ "}") . ("{" ++) . concat . intersperse ",") + . splitEvery s2 + . map ((++ "}\n ") . ("{" ++) . concat . intersperse ",") + . splitEvery s3 + . map ((++ "}\n ") . ("{" ++) . concat . intersperse ",") + . splitEvery s4 + . map ((++ "}\n ") . ("{" ++) . concat . intersperse ",") + . splitEvery s5 + $ map printNum xs + +block6 s2 s3 s4 s5 s6 xs + = (++ "};") + . ("{" ++) + . concat + . intersperse "\n," + . map ((++ "}") . ("{" ++) . concat . intersperse ",") + . splitEvery s2 + . map ((++ "}\n ") . ("{" ++) . concat . intersperse ",") + . splitEvery s3 + . map ((++ "}\n ") . ("{" ++) . concat . intersperse ",") + . splitEvery s4 + . map ((++ "}\n ") . ("{" ++) . concat . intersperse ",") + . splitEvery s5 + . map ((++ "}\n ") . ("{" ++) . concat . intersperse ",") + . splitEvery s6 + $ map printNum xs + + +pd :: String -> Double -> String +pd k v = printf "PUBLIC double %s=%f;" k v + +pi :: String -> Int -> String +pi k v = printf "PUBLIC int %s=%d;" k v + +printNum :: Int -> String +printNum n + | n >= maxN = " INF" + | otherwise = printf "%6d" n + where + maxN = 10000 diff --git a/Biobase/Vienna/Export/ViennaPar.hs b/Biobase/Vienna/Export/ViennaPar.hs --- a/Biobase/Vienna/Export/ViennaPar.hs +++ b/Biobase/Vienna/Export/ViennaPar.hs @@ -21,7 +21,7 @@ -export :: ViennaTables -> ViennaTables -> String +export :: ViennaIntTables -> ViennaIntTables -> String export trnr trnrH = hdr ++ blocks ++ mlps ++ ninios ++ misc ++ triloops ++ tetra ++ hexa ++ "\n#END" where hdr = "## RNAfold parameter file v2.0\n\n" mlps = printf "# ML_params\n%7d %7d %7d %7d %7d %7d\n\n" diff --git a/Biobase/Vienna/Import/Turner.hs b/Biobase/Vienna/Import/Turner.hs --- a/Biobase/Vienna/Import/Turner.hs +++ b/Biobase/Vienna/Import/Turner.hs @@ -20,7 +20,7 @@ import Biobase.Vienna -- | Convert from Turner keys to Vienna keys and all values from Double to Int -fromTurner :: TurnerTables -> ViennaTables +fromTurner :: TurnerTables -> ViennaIntTables fromTurner Turner2004{..} = Turner2004 { stack = convert pp stack , dangle3 = convert pb dangle3 @@ -43,7 +43,7 @@ , multiNuc = f2i multiNuc , multiHelix = f2i multiHelix , extMM = convert pbb extMM - , largeLoop = largeLoop + , largeLoop = largeLoop * 100 -- scale to decacals , termAU = f2i termAU , intermolecularInit = f2i intermolecularInit } diff --git a/Biobase/Vienna/Import/ViennaPar.hs b/Biobase/Vienna/Import/ViennaPar.hs --- a/Biobase/Vienna/Import/ViennaPar.hs +++ b/Biobase/Vienna/Import/ViennaPar.hs @@ -25,7 +25,7 @@ -- | Imports Vienna tables from a given string. -importPar :: String -> (ViennaTables,ViennaTables) +importPar :: String -> (ViennaIntTables,ViennaIntTables) importPar s | Right _ <- p = foldr updateTables (trnr,trnrH) bs | Left err <- p = error $ show err @@ -38,7 +38,7 @@ -- | Apply all parsed blocks to a Turner2004 structure. -updateTable :: Block -> ViennaTables -> ViennaTables +updateTable :: Block -> ViennaIntTables -> ViennaIntTables updateTable Block{..} trnr -- @Turner2004{..} | bhdr =? "stack" = trnr{stack = fromAssocs minBound maxBound z $ zip pp ints} | bhdr =? "dangle3" = trnr{dangle3 = fromAssocs minBound maxBound z $ zip pb ints} @@ -90,7 +90,7 @@ ppbbbb = [(p1,p2,b1,b2,b3,b4) | p1<-cguaP,p2<-cguaP,b1<-acgu,b2<-acgu,b3<-acgu,b4<-acgu] z = eInf -- xs is the block header name, ys the constant string -xs =? ys = xs == ys || xs == ys++"enthalpies" -- and $ zipWith (==) xs ys +xs =? ys = xs == ys || xs == ys++"_enthalpies" -- and $ zipWith (==) xs ys s2ns = map charToNucleotide -- * Simple parser for the vienna 2.0 format. diff --git a/Biobase/Vienna/Modification/NonStandard.hs b/Biobase/Vienna/Modification/NonStandard.hs --- a/Biobase/Vienna/Modification/NonStandard.hs +++ b/Biobase/Vienna/Modification/NonStandard.hs @@ -14,6 +14,7 @@ import Biobase.Turner.Tables import Data.Ix.Tuple import Biobase.Constants +import Biobase.Types.Energy import Data.PrimitiveArray @@ -23,7 +24,7 @@ changeTable f tbl = fromAssocs l u z . map (f tbl) $ assocs tbl where (l,u) = bounds tbl - z = eInf + z = Energy eInf @@ -33,7 +34,7 @@ fPPBBBBmax tbl (k@(p1,p2,b1,b2,b3,b4),v) | p1==vpNP || p2==vpNP = (k,v) -- don't do anything - | otherwise = (k,maximum + | otherwise = (k,maximum' [ tbl ! (p1n,p2n,b1n,b2n,b3n,b4n) | p1n <- genKeyP p1 , p2n <- genKeyP p2 @@ -45,7 +46,7 @@ fPPBBBmax tbl (k@(p1,p2,b1,b2,b3),v) | p1==vpNP || p2==vpNP = (k,v) - | otherwise = (k,maximum + | otherwise = (k,maximum' [ tbl ! (p1n,p2n,b1n,b2n,b3n) | p1n <- genKeyP p1 , p2n <- genKeyP p2 @@ -56,7 +57,7 @@ fPPBBmax tbl (k@(p1,p2,b1,b2),v) | p1==vpNP || p2==vpNP = (k,v) - | otherwise = (k,maximum + | otherwise = (k,maximum' [ tbl ! (p1n,p2n,b1n,b2n) | p1n <- genKeyP p1 , p2n <- genKeyP p2 @@ -66,7 +67,7 @@ fPPmax tbl (k@(p1,p2),v) | p1==vpNP || p2==vpNP = (k,v) - | otherwise = (k,maximum + | otherwise = (k,maximum' [ tbl ! (p1n,p2n) | p1n <- genKeyP p1 , p2n <- genKeyP p2 @@ -74,7 +75,7 @@ fPBBmax tbl (k@(p1,b1,b2),v) | p1==vpNP = (k,v) - | otherwise = (k,maximum + | otherwise = (k,maximum' [ tbl ! (p1n,b1n,b2n) | p1n <- genKeyP p1 , b1n <- genKeyB b1 @@ -83,12 +84,13 @@ fPBmax tbl (k@(p1,b1),v) | p1==vpNP = (k,v) - | otherwise = (k,maximum + | otherwise = (k,maximum' [ tbl ! (p1n,b1n) | p1n <- genKeyP p1 , b1n <- genKeyB b1 ]) +maximum' = Energy . maximum . map unEnergy -- * Generate keys. If the key is of the non-standard kind, then we go fishing, @@ -102,7 +104,7 @@ -- | The max operation applied to all relevant tables. (This serves as a -- pointer, which tables to manipulate). -nonStandardMax :: ViennaTables -> ViennaTables +nonStandardMax :: ViennaEnergyTables -> ViennaEnergyTables nonStandardMax tbl = tbl { iloop1x1 = changeTable fPPBBmax $ iloop1x1 tbl , iloop1x2 = changeTable fPPBBBmax $ iloop1x2 tbl diff --git a/Biobase/Vienna/Modification/Partition.hs b/Biobase/Vienna/Modification/Partition.hs new file mode 100644 --- /dev/null +++ b/Biobase/Vienna/Modification/Partition.hs @@ -0,0 +1,51 @@ + +-- | Small module for converting Vienna energy tables to partition function +-- value tables. +-- +-- Temperature scaling should happen on the level of energy tables, followed by +-- conversion here. +-- +-- TODO after the switch to the Energy type, change too, the partitionTables +-- generation + +module Biobase.Vienna.Modification.Partition + ( partitionTables + ) where + +import Biobase.Types.Partition +import Biobase.Types.Energy +import Biobase.Turner.Tables +import Biobase.Vienna +import Biobase.Constants + + +-- Testing + +{- +import Biobase.Vienna.Default +import Data.PrimitiveArray +import Debug.Trace.Tools +import Biobase.RNA +import Biobase.Types.Ring + +(g,h) = turner2004GH + +-- x = toList $ stack $ partitionTables 37 g +x = {- toList $ -} (stack $ partitionTables 37 g) ! (vpGC,vpGC) +-} + +-- | Create partition tables out of normal energy tables. Note that these +-- values are not normalized. An additional term 1/Z(1/kt) would be required +-- which is missing until we are done calculating the partition function. +-- +-- All energy contributions are rescaled from dekacals back to kcal/mol. +-- +-- We explicitly set all probabilities =0 where the energy is >= eMax. + +partitionTables :: Temperature -> ViennaEnergyTables -> ViennaPartitionTables +partitionTables tempe trnr = dmap f trnr where + kt = (tempe + kelvinC0) * gasconst + -- convert energy into probability; encapsulate as a (logFloat) partition + f (Energy e') = {- traceVal (show (e',e,p)) -} p where + e = fromIntegral e' / 100 + p = if e' >= eMax then Partition 0 else Partition . exp $ -e / kt -- can NOT use mkPartition as these values are NOT NORMALIZED diff --git a/Biobase/Vienna/Modification/Temperature.hs b/Biobase/Vienna/Modification/Temperature.hs --- a/Biobase/Vienna/Modification/Temperature.hs +++ b/Biobase/Vienna/Modification/Temperature.hs @@ -8,6 +8,7 @@ import Biobase.Vienna import Biobase.Turner.Tables +import Biobase.Constants @@ -20,12 +21,14 @@ -- TODO this does not take into account that dangles are supposed to _always_ -- be beneficial. We should therefor transform the energies and then apply 'min -- 0' onto all dangle types. +-- +-- TODO use EnergyTables (Int is just for im-/export) -adjustTemperature :: ViennaTables -> ViennaTables -> Temperature -> ViennaTables +adjustTemperature :: ViennaIntTables -> ViennaIntTables -> Temperature -> ViennaIntTables adjustTemperature trnrG trnrH cels = dZipWith f trnrG trnrH where f vG vH = let g = fromIntegral vG h = fromIntegral vH - k_0 = 273.15 + k_0 = kelvinC0 t_m = 37 + k_0 in round $ h - (h-g) * ((cels+k_0)/t_m) diff --git a/BiobaseVienna.cabal b/BiobaseVienna.cabal --- a/BiobaseVienna.cabal +++ b/BiobaseVienna.cabal @@ -1,10 +1,10 @@ name: BiobaseVienna -version: 0.0.2.1 +version: 0.0.2.3 author: Christian Hoener zu Siederdissen maintainer: choener@tbi.univie.ac.at copyright: Christian Hoener zu Siederdissen, 2010 category: Bioinformatics -synopsis: ViennaRNA parameter library +synopsis: (deprecated) ViennaRNA parameter library license: GPL-3 license-file: LICENSE build-type: Simple @@ -28,6 +28,7 @@ split >=0.1.2, tuple >=0.2.0.1, vector >=0.7 && <0.8, + directory >=1, PrimitiveArray >=0.0.2 && <0.0.3, ParsecTools >=0.0.2 && <0.0.3, @@ -41,8 +42,10 @@ Biobase.Vienna.Import.Turner Biobase.Vienna.Import.ViennaPar Biobase.Vienna.Export.ViennaPar + Biobase.Vienna.Export.ViennaC Biobase.Vienna.Modification.NonStandard Biobase.Vienna.Modification.Temperature + Biobase.Vienna.Modification.Partition Biobase.Vienna.Default ghc-options: diff --git a/templates/cheader b/templates/cheader --- a/templates/cheader +++ b/templates/cheader @@ -2,9 +2,15 @@ /* Automatically generated using the TurnerParser - TurnerParser (c) 2008,2009 + TurnerParser (c) 2008,2009,2010 Christian Hoener zu Siederdissen, TBI Vienna choener (at) tbi.univie.ac.at + + The library enabling this can be found at: + http://hackage.haskell.org/package/BiobaseVienna + the program can be found at: + (sorry, not yet) + install using cabal: cabal install (sorry, not yet) */ /* @@ -18,7 +24,7 @@ Enthalpies taken from: A. Walter, D Turner, J Kim, M Lyttle, P M"uller, D Mathews, M Zuker - "Coaxial stckaing of helices enhances binding of oligoribonucleotides.." + "Coaxial stacking of helices enhances binding of oligoribonucleotides.." PNAS, 91, pp 9218-9222, 1994 D.H. Turner, N. Sugimoto, and S.M. Freier. @@ -30,7 +36,7 @@ PNAS, 86, 7706-7710, October 1989. L. He, R. Kierzek, J. SantaLucia, A.E. Walter, D.H. Turner - "Nearest-Neughbor Parameters for GU Mismatches...." + "Nearest-Neighbor Parameters for GU Mismatches...." Biochemistry 1991, 30 11124-11132 A.E. Peritz, R. Kierzek, N, Sugimoto, D.H. Turner