RUJ       !"#$%&'()*+,-./0 1 2 3 4 5 6 7 8 9 : ; < = > ? @ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z [ \ ] ^ _ ` a b c d e f g hijklmnopqrstuvwxyz{|}~Safe=Parse nucleotide sequence. Allowed letters according to IUPACeParse nucleotide alignment entry. Allowed letters according to IUPAC and commonly used gap charactersJParse protein amino acid code sequence. Allowed letters according to IUPACrParse protein amino acid code alignment entry. Allowed letters according to IUPAC and commonly used gap charactersSafe5Data structure for (sub-) optimal interaction region Data structure for individual interaction between a target and query nucleic acid seqence, contains all (sub)-optimal interactions      Safe4Parse the input as list of RNAupInteraction datatype,Parse the consenus of RNAup results Parse a RNAupInteractionRegionParse a RNAupFileName#parse RNAupOutput from input string/parse from input filePath  SafeData structureSafe+Parse the consenus of RNAz results *parse RNAdistance output from input stringBparse RNAdistance output from input filePath Safe Data structure corrsponds with alifoldoutput redirected to file. Output written directly to commandline also contains number of sequences and length of consensus sequence !"#$%& !"#$%& !"#$%& !"#$%&Safe+Parse the consenus of RNAz results ()parse RNAalifold output from input string)Aparse RNAalifold output from input filePath '() !"#$%&'()'()'()Safe*Data structure for RNAfold*+,-./*+,-./*+,-./*+,-./ Safe0PRun external RNAfold command and read the output into the corresponding datatype+Parse the consenus of RNAz results 1&parse RNAfold output from input string2>parse RNAfold output from input filePath 012 *+,-./012012012 Safe3IDatatype contains all elements for the consenus result of input alignment7XDatatype contains all result elements for each member of the input alignment ?;All elements of RNAz output are contained in this datatype #3456789:;<=>?@ABCDEFGHIJKLMNOPQRSTU#3456789:;<=>?@ABCDEFGHIJKLMNOPQRSTU#?@ABCDEFGHIJKLMNOPQRSTU789:;<=>34563456789:;<=>?@ABCDEFGHIJKLMNOPQRSTU Safe VMRun external RNAz command and read the output into the corresponding datatype Parse the input as RNAz datatype'Parse a RNAz field containing a Double /Parse a RNAz field containing a String -Parse a RNAz field containing a Int Parse a RNAz result +Parse the consenus of RNAz results Wparse RNAz from input stringX/parse from input filePath VWX&3456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXVWX VWX SafeYYData structure for individual interaction between a target and query nucleic acid seqence YZ[\]^_`abcde YZ[\]^_`abcde YZ[\]^_`abcdeY Z[\]^_`abcde Safe6Parse the input as list of RNAplexInteraction datatype.Parse the consenus of RNAplex results f%parse RNAplexOutput from input stringg/parse from input filePath fgYZ[\]^_`abcdefgfgfgSafeh8Data structure for cofolding of 2 nucleic acid sequenceshijklmnhijklmnhijklmnhijklmnSafeoRun external RNAcofold command 0Parse the consenus of RNAcofold results p(parse RNAcofold output from input stringq@parse RNAcofold output from input filePath opq hijklmnopqopqopqSafer RNAcode Hit~>All elements of RNAcode output are contained in this datatype rstuvwxyz{|}~rstuvwxyz{|}~~rstuvwxyz{|}r stuvwxyz{|}~ Safe PRun external RNAcode command and read the output into the corresponding datatype+Parse the tabular input as RNAcode datatypeParse the input as RNAcodeHit#Parse the input as RNAcode datatypeParse the input as RNAcodeHitparse RNAcode from input string7parse RNAcode from input filePath parse RNAcode from input string7parse RNAcode from input filePath rstuvwxyz{|}~ Safe  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ !"#$%&&'()*+,,-./001234567899:;<= > ? @ A A B C D D E F G H I J K K L M N O P Q R S T U V W X Y Z [ \ ] ^ _ ` a b c d d e f g h i j k l m n o p qrrstuvwxyz{{|}~ Vienn_55fJKJjovrR0yDOGtoMY8HBio.ViennaRNAParserLibrary Bio.RNAupDataBio.RNAupParserBio.RNAdistanceDataBio.RNAdistanceParserBio.RNAalifoldDataBio.RNAalifoldParserBio.RNAfoldDataBio.RNAfoldParser Bio.RNAzDataBio.RNAzParserBio.RNAplexDataBio.RNAplexParserBio.RNAcofoldDataBio.RNAcofoldParserBio.RNAcodeDataBio.RNAcodeParserBio.ViennaRNAParser readDoublereadIntparseNucleotideSequenceparseNucleotideAlignmentEntryparseProteinSequenceparseProteinAlignmentEntryRNAupInteractionRegionupSecondaryStructureupQueryDuplexBeginupQueryDuplexEndupTargetDuplexBeginupTargetDuplexEndupDuplexEnergy!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 readRNAcofold RNAcodeHithssframelengthfromtonamestartendscorepvalueRNAcode rnacodeHitsrcAlignmentNumberrcTimercSampleNumberrcDelta rcBigOmega rcSmallOmega rcStopPenalty systemRNAcode parseRNAcode readRNAcodeparseRNAcodeTabularreadRNAcodeTabularparseRNAupOutputparseRNAupInteractionparseRNAupInteractionRegionparseRNAupFileNamegenParserRNAdistancegenParserRNAalifoldgenParserRNAfold genParseRNAzparseRNAzDoubleFieldparseRNAzStringFieldparseRNAzIntFieldparseRNAzResultparseRNAzConsensusparseRNAplexOutputparseRNAplexInteractiongenParserRNAcofoldgenParseRNAcodeTabulargenParseRNAcodeTabularHitgenParseRNAcodegenParseRNAcodeHit