úÎFă@Ar      !"#$%&'()*+,-./0 1 2 3 4 5 6 7 8 9 : ; < = > ? @ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z [ \ ] ^ _ ` a b c d e f g hijklmnopq Safe-Inferred=Parse nucleotide sequence. Allowed letters according to IUPACeParse nucleotide alignment entry. Allowed letters according to IUPAC and commonly used gap charactersJParse protein amino acid code sequence. Allowed letters according to IUPACrParse protein amino acid code alignment entry. Allowed letters according to IUPAC and commonly used gap characters Safe-Inferred5Data structure for (sub-) optimal interaction region ƒData structure for individual interaction between a target and query nucleic acid seqence, contains all (sub)-optimal interactions       Safe-Inferredr4Parse the input as list of RNAupInteraction datatypes,Parse the consenus of RNAup results tParse a RNAupInteractionRegionuParse a RNAupFileName#parse RNAupOutput from input string/parse from input filePath rstu rstu Safe-InferredData structure Safe-Inferredv+Parse the consenus of RNAz results *parse RNAdistance output from input stringBparse RNAdistance output from input filePath vv Safe-Inferred ŞData structure corrsponds with alifoldoutput redirected to file. Output written directly to commandline also contains number of sequences and length of consensus sequence !"#$%& !"#$%& !"#$%& !"#$%& Safe-Inferredw+Parse the consenus of RNAz results ()parse RNAalifold output from input string)Aparse RNAalifold output from input filePath 'w() !"#$%&'()'()'w() Safe-Inferred*Data structure for RNAfold*+,-./*+,-./*+,-./*+,-./  Safe-Inferred0PRun external RNAfold command and read the output into the corresponding datatypex+Parse the consenus of RNAz results 1&parse RNAfold output from input string2>parse RNAfold output from input filePath 0x12 *+,-./0120120x12  Safe-Inferred3IDatatype 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-Inferred VMRun external RNAz command and read the output into the corresponding datatypey Parse the input as RNAz datatypez'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 Vyz{|}~WX&3456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXVWX Vyz{|}~WX  Safe-InferredYYData structure for individual interaction between a target and query nucleic acid seqence YZ[\]^_`abcde YZ[\]^_`abcde YZ[\]^_`abcdeY Z[\]^_`abcde  Safe-Inferred6Parse the input as list of RNAplexInteraction datatype€.Parse the consenus of RNAplex results f%parse RNAplexOutput from input stringg/parse from input filePath €fgYZ[\]^_`abcdefgfg€fg Safe-Inferredh8Data structure for cofolding of 2 nucleic acid sequenceshijklmnhijklmnhijklmnhijklmn Safe-InferredoRun external RNAcofold command 0Parse the consenus of RNAcofold results p(parse RNAcofold output from input stringq@parse RNAcofold output from input filePath opq hijklmnopqopqopq Safe-Inferredl  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopq‚ !"#$$%&'()**+,-../01234567789:; < = > ? ? @ A B B C D E F G H I I J K L M N O P Q R S T U V W X Y Z [ \ ] ^ _ ` a b b c d e f g h i j k l m n oppqrstuvwxyz{|}~  €  ‚ ƒ „ … † ‡ˆ‰ViennaRNAParser-1.2.4Bio.ViennaRNAParserLibrary Bio.RNAupDataBio.RNAupParserBio.RNAdistanceDataBio.RNAdistanceParserBio.RNAalifoldDataBio.RNAalifoldParserBio.RNAfoldDataBio.RNAfoldParser Bio.RNAzDataBio.RNAzParserBio.RNAplexDataBio.RNAplexParserBio.RNAcofoldDataBio.RNAcofoldParserBio.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 readRNAcofoldparseRNAupOutputparseRNAupInteractionparseRNAupInteractionRegionparseRNAupFileNamegenParserRNAdistancegenParserRNAalifoldgenParserRNAfold genParseRNAzparseRNAzDoubleFieldparseRNAzStringFieldparseRNAzIntFieldparseRNAzResultparseRNAzConsensusparseRNAplexOutputparseRNAplexInteractiongenParserRNAcofold