@:l      !"#$%&'()*+,- . / 0 1 2 3 4 5 6 7 8 9 : ; < = > ? @ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z [ \ ] ^ _ ` a b c d e f g h ijk Safe-Inferred5Data structure for (sub-) optimal interaction region Data structure for individual interaction between a target and query nucleic acid seqence, contains all (sub)-optimal interactions       Safe-Inferredl4Parse the input as list of RNAupInteraction datatypem,Parse the consenus of RNAup results nParse a RNAupInteractionRegionoParse a RNAupFileName#parse RNAupOutput from input string/parse from input filePath pqlmno pqlmno Safe-InferredData structure Safe-Inferredr+Parse the consenus of RNAz results *parse RNAdistance output from input stringBparse RNAdistance output from input filePath srsr Safe-InferredData structure corrsponds with alifoldoutput redirected to file. Output written directly to commandline also contains number of sequences and length of consensus sequence     Safe-Inferredt+Parse the consenus of RNAz results ")parse RNAalifold output from input string#Aparse RNAalifold output from input filePath u!t"#  !"#!"#u!t"# Safe-Inferred$Data structure for RNAfold$%&'()$%&'()$%&'()$%&'() Safe-Inferred*PRun external RNAfold command and read the output into the corresponding datatypev+Parse the consenus of RNAz results +&parse RNAfold output from input string,>parse RNAfold output from input filePath *wv+, $%&'()*+,*+,*wv+,  Safe-Inferred-IDatatype contains all elements for the consenus result of input alignment1XDatatype contains all result elements for each member of the input alignment 9;All elements of RNAz output are contained in this datatype #-./0123456789:;<=>?@ABCDEFGHIJKLMNO#-./0123456789:;<=>?@ABCDEFGHIJKLMNO#9:;<=>?@ABCDEFGHIJKLMNO12345678-./0-./0123456789:;<=>?@ABCDEFGHIJKLMNO  Safe-Inferred PMRun external RNAz command and read the output into the corresponding datatypex Parse the input as RNAz datatypey'Parse a RNAz field containing a Double z/Parse a RNAz field containing a String {-Parse a RNAz field containing a Int |Parse a RNAz result }+Parse the consenus of RNAz results Qparse RNAz from input stringR/parse from input filePath ~Pxyz{|}QR&-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRPQR ~Pxyz{|}QR  Safe-InferredSYData structure for individual interaction between a target and query nucleic acid seqence STUVWXYZ[\]^_ STUVWXYZ[\]^_ STUVWXYZ[\]^_S TUVWXYZ[\]^_  Safe-Inferred6Parse the input as list of RNAplexInteraction datatype.Parse the consenus of RNAplex results `%parse RNAplexOutput from input stringa/parse from input filePath `aSTUVWXYZ[\]^_`a`a`a  Safe-Inferredb8Data structure for cofolding of 2 nucleic acid sequencesbcdefghbcdefghbcdefghbcdefgh Safe-InferrediRun external RNAcofold command 0Parse the consenus of RNAcofold results j(parse RNAcofold output from input stringk@parse RNAcofold output from input filePath ijk bcdefghijkijkijk Safe-Inferredl  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijk !"##$%&''()*+,-./001234567 8 8 9 : ; ; < = > ? @ A B B C D E F G H I J K L M N O P Q R S T U V W X Y Z [ [ \ ] ^ _ ` a b c d e f g h i i j k l m nopqrstuvwxwyvzv { | } ~  v w v wvViennaRNAParser-1.2.0 Bio.RNAupDataBio.RNAupParserBio.RNAdistanceDataBio.RNAdistanceParserBio.RNAalifoldDataBio.RNAalifoldParserBio.RNAfoldDataBio.RNAfoldParser Bio.RNAzDataBio.RNAzParserBio.RNAplexDataBio.RNAplexParserBio.RNAcofoldDataBio.RNAcofoldParserBio.ViennaRNAParserRNAupInteractionRegionupSecondaryStructureupQueryDuplexBeginupQueryDuplexEndupTargetDuplexBeginupTargetDuplexEndupDuplexEnergy!upDuplexEnergyWithoutAccessiblityupQueryAccessiblityupTargetAccessibilityupQuerySequenceupTargetSequenceupOutputFileNameRNAupInteractionupQueryIdentifierupTargetIdentifierupInteractions parseRNAup readRNAup RNAdistancesecondaryStructureDistanceparseRNAdistancereadRNAdistance RNAalifoldalignmentConsensusSequencealignmentConsensusDotBracket#alignmentConsensusMinimumFreeEnergy*alignmentConsensusInitialMinimumFreeEnergy/alignmentConsensusEnergyCovarianceContributionssystemRNAalifoldparseRNAalifoldreadRNAalifoldRNAfoldsequenceIdentifier foldSequencefoldSecondaryStructure foldingEnergy systemRNAfold parseRNAfold readRNAfold RNAzConsensusconsensusSequenceconsensusDotBracket RNAzResultheaderresultSequence dotBracketminimumFreeEnergyzScorezscoreCalculationApproachRNAzversionsequenceNumber columnNumberreadingDirectionmeanPairwiseIdentityshannonEntropy gcContent#meanSingleSequenceMinimumFreeEnergyconsensusMinimumFreeEnergyenergyContributioncovarianceContributioncombinationsPair meanZScorestructureConservationIndexbackgroundModel decisionModelsvmDecisionValuesvmRNAClassProbability prediction rnazResults rnazConsensus systemRNAz parseRNAzreadRNAzRNAplexInteractiontargetIdentifierqueryIdentifierplexSecondaryStructuretargetDuplexBegintargetDuplexEndqueryDuplexBeginqueryDuplexEnd duplexEnergyduplexEnergyWithoutAccessiblityqueryAccessiblitytargetAccessibility parseRNAplex readRNAplex RNAcofoldcoFoldSequence1coFoldSequence2coFoldSecondaryStructure1coFoldSecondaryStructure2coFoldingEnergysystemRNAcofoldparseRNAcofold readRNAcofoldparseRNAupOutputparseRNAupInteractionparseRNAupInteractionRegionparseRNAupFileName readDoublereadIntgenParserRNAdistancegenParserRNAalifoldgenParserRNAfold genParseRNAzparseRNAzDoubleFieldparseRNAzStringFieldparseRNAzIntFieldparseRNAzResultparseRNAzConsensusparseRNAplexOutputparseRNAplexInteractiongenParserRNAcofold