úÎUuKÔŠ      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefg h i j k l m n o p q r s t u v w x y z { | }~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜™š›œžŸ Ą˘Ł¤ĽŚ§¨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 datatypeŠ Parse the input as RNAz datatypeŞ'Parse a RNAz field containing a Double Ť/Parse a RNAz field containing a String Ź-Parse a RNAz field containing a Int ­Parse a RNAz result Ž+Parse the consenus of RNAz results 0parse RNAz from input string1/parse from input filePath /ŠŞŤŹ­Ž01&  !"#$%&'(/01/01 /ŠŞŤŹ­Ž01Safe25Data structure for (sub-) optimal interaction region @ƒData structure for individual interaction between a target and query nucleic acid seqence, contains all (sub)-optimal interactions 23456789:;<=>?@ABCD23456789:;<=>?@ABCD@ABCD23456789:;<=>?2 3456789:;<=>?@ABCDSafeŻ4Parse the input as list of RNAupInteraction datatype°,Parse the consenus of RNAup results ąParse a RNAupInteractionRegion˛Parse a RNAupFileNameI#parse RNAupOutput from input stringJ/parse from input filePath ݰą˛IJ23456789:;<=>?@ABCDIJIJݰą˛IJSafeKYData structure for individual interaction between a target and query nucleic acid seqenceKLMNOPQRSTUVWXYZKLNMOPQRSTUVWXYZKLMNOPQRSTUVWXYZKLMNOPQRSTUVWXYZSafeł6Parse the input as list of RNAplexInteraction datatype´.Parse the consenus of RNAplex results ]%parse RNAplexOutput from input string^/parse from input filePath ł´]^KLNMOPQRSTUVWXYZ]^]^ł´]^Safe_Data structure for RNAfold_`abcd_`abcd_`abcd_`abcd SafegPRun external RNAfold command and read the output into the corresponding datatypeľ+Parse the consenus of RNAz results h&parse RNAfold output from input stringi>parse RNAfold output from input filePath gľhi _`abcdghighigľhi SafejData structurejkljkljkljkl Safeś+Parse the consenus of RNAz results o*parse RNAdistance output from input stringpBparse RNAdistance output from input filePath śopjklopopśop Safeq8Data structure for cofolding of 2 nucleic acid sequencesqrstuvwqrstuvwqrstuvwqrstuvw SafezRun external RNAcofold command ˇ0Parse the consenus of RNAcofold results {(parse RNAcofold output from input string|@parse RNAcofold output from input filePath zˇ{| qrstuvwz{|z{|zˇ{|Safe} RNAcode HitŠ>All elements of RNAcode output are contained in this datatype }~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“}~ƒ„‡…€‚†ˆ‰Š‹ŒŽ‘’“Š‹ŒŽ‘’“}~€‚ƒ„…†‡ˆ‰} ~€‚ƒ„…†‡ˆ‰Š ‹ŒŽ‘’“Safe ˜PRun external RNAcode command and read the output into the corresponding datatype¸+Parse the tabular input as RNAcode datatypešParse the input as RNAcodeHitş#Parse the input as RNAcode datatypeťParse the input as RNAcodeHit™parse RNAcode from input stringš7parse RNAcode from input filePath ›parse RNAcode from input stringœ7parse RNAcode from input filePath ˜¸šşť™š›œ}~ƒ„‡…€‚†ˆ‰Š‹ŒŽ‘’“˜™š›œ˜™š›œ ˜¸šşť™š›œSafeŞData structure corrsponds with alifoldoutput redirected to file. Output written directly to commandline also contains number of sequences and length of consensus sequencežŸ Ą˘ŁžŸ Ą˘ŁžŸ Ą˘ŁžŸ Ą˘ŁSafeź+Parse the consenus of RNAz results §)parse RNAalifold output from input string¨Aparse RNAalifold output from input filePath Śź§¨ žŸ Ą˘ŁŚ§¨ڧ¨Śź§¨Safe‹  !"#$%&'(/0123456789:;<=>?@ABCDIJKLNMOPQRSTUVWXYZ]^_`abcdghijklopqrstuvwz{|}~ƒ„‡…€‚†ˆ‰Š‹ŒŽ‘’“˜™š›œžŸ Ą˘ŁŚ§¨˝ !"##$%&'()*+,-./0123456789:;<=>?@ABBCDEFGHIJKLMNOOPQRSTUVWXYYZ[\]^_`abcdefghijkllmnopqr s t u v v w x y z { | | } ~  €  ‚ ƒ „ … †‡‡ˆ‰Š‹ŒŽ‘’““”•–—˜™š›œžŸ Ą˘Ł¤ĽĽŚ§¨ŠŞŤŹ­ŽŻ°ą˛ł´ľśˇ¸šşť ź ˝ žżŔÁÂĂÄ,ViennaRNAParser-1.3.2-9JTEtgv4lOh7katC0EyqbSBio.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 readRNAplexRNAfoldsequenceIdentifier foldSequencefoldSecondaryStructure foldingEnergy $fShowRNAfold $fEqRNAfold systemRNAfold parseRNAfold readRNAfold RNAdistancesecondaryStructureDistance$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 genParseRNAzparseRNAzDoubleFieldparseRNAzStringFieldparseRNAzIntFieldparseRNAzResultparseRNAzConsensusparseRNAupOutputparseRNAupInteractionparseRNAupInteractionRegionparseRNAupFileNameparseRNAplexOutputparseRNAplexInteractiongenParserRNAfoldgenParserRNAdistancegenParserRNAcofoldgenParseRNAcodeTabulargenParseRNAcodeTabularHitgenParseRNAcodegenParseRNAcodeHitgenParserRNAalifold