\R!      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxy z { | } ~  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 charactersSafeIDatatype contains all elements for the consenus result of input alignment XDatatype contains all result elements for each member of the input alignment ;All elements of RNAz output are contained in this datatype #  !"#$%&'(#  !"#$%&'(# !"#$%&'(     !"#$%&'(Safe /MRun 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 0parse RNAz from input string1/parse from input filePath /01&  !"#$%&'(/01/01 /01Safe25Data structure for (sub-) optimal interaction region @Data structure for individual interaction between a target and query nucleic acid seqence, contains all (sub)-optimal interactions 23456789:;<=>?@ABCD23456789:;<=>?@ABCD@ABCD23456789:;<=>?2 3456789:;<=>?@ABCDSafe4Parse the input as list of RNAupInteraction datatype,Parse the consenus of RNAup results Parse a RNAupInteractionRegionParse a RNAupFileNameI#parse RNAupOutput from input stringJ/parse from input filePath IJ23456789:;<=>?@ABCDIJIJIJSafeKYData structure for individual interaction between a target and query nucleic acid seqenceKLMNOPQRSTUVWXYZKLNMOPQRSTUVWXYZKLMNOPQRSTUVWXYZKLMNOPQRSTUVWXYZSafe6Parse the input as list of RNAplexInteraction datatype.Parse the consenus of RNAplex results ]%parse RNAplexOutput from input string^/parse from input filePath ]^KLNMOPQRSTUVWXYZ]^]^]^SafeoData structure for RNAfold_`abcdefghijklmnopqrst_`abcdefghijklmnopqrstopqrst_`abcdefghijklmn_`abcdefghijklmnopqrst SafeyPRun external RNAfold command and read the output into the corresponding datatypezPRun external RNAfold command and read the output into the corresponding datatypeParse the RNAfold results{&parse RNAfold output from input string|>parse RNAfold output from input filePath 3Parse the RNAfold maximum expected accuracy results}&parse RNAfold output from input string~>parse RNAfold output from input filePath yz{|}~_`abcdefghijklmnopqrstyz{|}~y{|z}~yz{|}~ SafeData structure Safe+Parse the consenus of RNAz results *parse RNAdistance output from input stringBparse RNAdistance output from input filePath  Safe8Data structure for cofolding of 2 nucleic acid sequences SafeRun external RNAcofold command 0Parse the consenus of RNAcofold results (parse RNAcofold output from input string@parse RNAcofold output from input filePath  Safe RNAcode Hit>All elements of RNAcode output are contained in this datatype  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  SafeData structure corrsponds with alifoldoutput redirected to file. Output written directly to commandline also contains number of sequences and length of consensus sequenceSafe+Parse the consenus of RNAz results )parse RNAalifold output from input stringAparse RNAalifold output from input filePath  Safe  !"#$%&'(/0123456789:;<=>?@ABCDIJKLNMOPQRSTUVWXYZ]^_`abcdefghijklmnopqrstyz{|}~ !"##$%&'()*+,-./0123456789:;<=>?@ABBCDEFGHIJKLMNOOPQRSTUVWXYYZ[\]^_`abcdefghijkllmnopqrstuvwxyz{{|}~      ,ViennaRNAParser-1.3.3-Jrm9vhxdjRFDxuQARsmHBvBio.ViennaRNAParserLibrary Bio.RNAzDataBio.RNAzParser Bio.RNAupDataBio.RNAupParserBio.RNAplexDataBio.RNAplexParserBio.RNAfoldDataBio.RNAfoldParserBio.RNAdistanceDataBio.RNAdistanceParserBio.RNAcofoldDataBio.RNAcofoldParserBio.RNAcodeDataBio.RNAcodeParserBio.RNAalifoldDataBio.RNAalifoldParserBio.ViennaRNAParser readDoublereadIntparseNucleotideSequenceparseNucleotideAlignmentEntryparseProteinSequenceparseProteinAlignmentEntry RNAzConsensusconsensusSequenceconsensusDotBracket RNAzResultheaderresultSequence dotBracketminimumFreeEnergyzScorezscoreCalculationApproachRNAzversionsequenceNumber columnNumberreadingDirectionmeanPairwiseIdentityshannonEntropy gcContent#meanSingleSequenceMinimumFreeEnergyconsensusMinimumFreeEnergyenergyContributioncovarianceContributioncombinationsPair meanZScorestructureConservationIndexbackgroundModel decisionModelsvmDecisionValuesvmRNAClassProbability prediction rnazResults rnazConsensus$fShowRNAzResult$fEqRNAzResult$fShowRNAzConsensus$fEqRNAzConsensus $fShowRNAz$fEqRNAz systemRNAz parseRNAzreadRNAzRNAupInteractionRegionupSecondaryStructureupQueryDuplexBeginupQueryDuplexEndupTargetDuplexBeginupTargetDuplexEndupDuplexEnergy!upDuplexEnergyWithoutAccessiblityupQueryAccessiblityupTargetAccessibilityupQuerySequenceupTargetSequenceupOutputFileNameRNAupInteractionupQueryIdentifierupTargetIdentifierupInteractions$fShowRNAupInteractionRegion$fEqRNAupInteractionRegion$fShowRNAupInteraction$fEqRNAupInteraction parseRNAup readRNAupRNAplexInteractiontargetIdentifierqueryIdentifierplexSecondaryStructuretargetDuplexBegintargetDuplexEndqueryDuplexBeginqueryDuplexEnd duplexEnergyduplexEnergyWithoutAccessiblityqueryAccessiblitytargetAccessibilityprefilterStart prefilterStopprefilterEnergy$fShowRNAplexInteraction$fEqRNAplexInteraction parseRNAplex readRNAplex RNAfoldMEAmeaSequenceIdentifiermeaFoldSequence mfeStructuremfefoldingEnergycoarseStructurecoarseFoldingEnergycentroidStructurecentroidFoldingEnergycentroidDistance meaStructuremeaFoldingEnergy meaDistancemfeFreqensembleDiversityRNAfoldsequenceIdentifier foldSequencefoldSecondaryStructure foldingEnergy $fShowRNAfold $fEqRNAfold$fShowRNAfoldMEA$fEqRNAfoldMEA systemRNAfoldsystemRNAfoldOptions parseRNAfold readRNAfoldparseRNAMEAfoldreadRNAMEAfold RNAdistancesecondaryStructureDistance$fShowRNAdistance$fEqRNAdistanceparseRNAdistancereadRNAdistance RNAcofoldcoFoldSequence1coFoldSequence2coFoldSecondaryStructure1coFoldSecondaryStructure2coFoldingEnergy$fShowRNAcofold $fEqRNAcofoldsystemRNAcofoldparseRNAcofold readRNAcofold RNAcodeHithssstrandframe hitLengthfromtonamestartendscorepvalueRNAcode rnacodeHitsrcAlignmentNumberrcTimercSampleNumberrcDelta rcBigOmega rcSmallOmega rcStopPenalty$fShowRNAcodeHit$fEqRNAcodeHit $fShowRNAcode $fEqRNAcode systemRNAcode parseRNAcode readRNAcodeparseRNAcodeTabularreadRNAcodeTabular RNAalifoldalignmentConsensusSequencealignmentConsensusDotBracket#alignmentConsensusMinimumFreeEnergy*alignmentConsensusInitialMinimumFreeEnergy/alignmentConsensusEnergyCovarianceContributions$fShowRNAalifold$fEqRNAalifoldsystemRNAalifoldparseRNAalifoldreadRNAalifold genParseRNAzparseRNAzDoubleFieldparseRNAzStringFieldparseRNAzIntFieldparseRNAzResultparseRNAzConsensusparseRNAupOutputparseRNAupInteractionparseRNAupInteractionRegionparseRNAupFileNameparseRNAplexOutputparseRNAplexInteractiongenParserRNAfoldgenParserRNAMEAfoldgenParserRNAdistancegenParserRNAcofoldgenParseRNAcodeTabulargenParseRNAcodeTabularHitgenParseRNAcodegenParseRNAcodeHitgenParserRNAalifold