ViennaRNA Package 2.0 英文参考文献.docVIP

Lorenzetal.AlgorithmsforMolecularBiology2011,6:26 /content/6/1/26 SOFTWARE ARTICLE OpenAccess ViennaRNAPackage2.0 RonnyLorenz1*,StephanHBernhart1,ChristianH?nerzuSiederdissen1,HakimTafer2,ChristophFlamm1, PeterFStadler2,1,3,4,5,6 andIvoLHofacker1,3,7* Abstract Background:Secondarystructureformsanimportantintermediatelevelofdescriptionofnucleicacidsthat encapsulatesthedominatingpartofthefoldingenergy,isoftenwellconservedinevolution,andisroutinelyused asabasistoexplainexperimentalfindings.Basedoncarefullymeasuredthermodynamicparameters,exact dynamicprogrammingalgorithmscanbeusedtocomputegroundstates,basepairingprobabilities,aswellas thermodynamicproperties. Results:TheViennaRNAPackagehasbeenawidelyusedcompilationofRNAsecondarystructurerelated computerprogramsfornearlytwodecades.Majorchangesinthestructureofthestandardenergymodel,the Turner2004parameters,thepervasiveuseofmulti-coreCPUs,andanincreasingnumberofalgorithmicvariants promptedamajortechnicaloverhaulofboththeunderlyingRNAlibandtheinteractiveuserprograms.New featuresincludeanexpandedrepertoireoftoolstoassessRNA-RNAinteractionsandrestrictedensemblesof structures,additionaloutputinformationsuchascentroidstructuresandmaximumexpectedaccuracystructures derivedfrombasepairingprobabilities,orz-scoresforlocallystablesecondarystructures,andsupportforinputin fastaformat.Updateswereimplementedwithoutcompromisingthecomputationalefficiencyofthecore algorithmsandensuringcompatibilitywithearlierversions. Conclusions:TheViennaRNAPackage2.0,supportingconcurrentcomputationsviaOpenMP,canbe downloadedfromhttp://www.tbi.univie.ac.at/RNA. Background beapproximatedasahierarchicalprocessinwhichsec- Atypical single stranded-nucleic acidmolecule hasthe ondarystructureisformedbeforetertiarystructure[1]. propensitytoformdoublehelicalstructurescausingthe The dominance of base pairing and the confinement molecule tofold back onto itself. Simple rules ofcom- to a single interaction partner makes it possible to plementary base pairing go