ts-dna - v2.4.0

Index

Enumerations

AminoAcidCharge AminoAcidPolarity AminoAcidSideChainType EnzymeType NucleicAcidType

Classes

AminoAcid DNA DNALigase DNAPolymerase Enzyme EnzymeFactory Exonuclease ForkCoordinator Gene Helicase IntervalNode IntervalTree InvalidCodonError InvalidNucleotidePatternError InvalidSequenceError LaggingStrandSynthesis LeadingStrandSynthesis MRNA NucleicAcid NucleotidePattern NucleotidePatternSymbol OkazakiFragment Polypeptide PreMRNA Primase ProcessedRNA Promoter PromoterElement RNA RNAPrimer ReplicationFork Replisome SpliceVariantPatterns SplicingOutcome

Interfaces

AlternativeSplicingOptions AlternativeSplicingProfile AminoAcidData CleavageSiteOptions EnzymePosition GenomicRegion OrganismProfile PolyadenylationSite PromoterSearchOptions RNAProcessingOptions ReplicationEvent ReplicationOptions ReplicationResult ReplicationRuntimeState ReplicationState ReplisomeConfig SimpleReplicationOptions SpliceVariant TranscriptionOptions

Type Aliases

ValidationResult

Variables

ACCEPTOR_SPLICE_CONSENSUS AP1_SITE AP1_SITE_CONSENSUS AP1_SITE_NAME AU_RICH_CONTEXT_BOOST BASE_POLYA_SCORE CAAT_BOX CAAT_BOX_CONSENSUS CAAT_BOX_NAME CAAT_ELEMENT_SCORE_BOOST CANONICAL_POLYA_SIGNAL_DNA CEBP_SITE CEBP_SITE_CONSENSUS CEBP_SITE_NAME CLEAVAGE_CONTEXT_WINDOW CODON_LENGTH CODON_TO_SINGLE_LETTER_CODE_MAP CORE_PROMOTER_ELEMENTS DEFAULT_ALTERNATIVE_SPLICING_OPTIONS DEFAULT_CLEAVAGE_DISTANCE_RANGE DEFAULT_CLEAVAGE_OFFSET DEFAULT_CLEAVAGE_OPTIONS DEFAULT_CLEAVAGE_PREFERENCE DEFAULT_DOWNSTREAM_DSE_PATTERN DEFAULT_DOWNSTREAM_SEARCH_DISTANCE DEFAULT_MAX_INTRON_SEARCH DEFAULT_MAX_PROMOTER_SEARCH_DISTANCE DEFAULT_MIN_PROMOTER_STRENGTH DEFAULT_POLYA_SIGNALS DEFAULT_POLYA_SIGNAL_STRENGTH DEFAULT_POLY_A_TAIL_LENGTH DEFAULT_RNA_PROCESSING_OPTIONS DEFAULT_UPSTREAM_USE_PATTERN DNA_POL_III_SPEED_FACTOR DNA_POL_II_SPEED_FACTOR DNA_POL_I_SPEED_FACTOR DNA_PROOFREADING_THRESHOLD DONOR_SPLICE_CONSENSUS DOWNSTREAM_PROMOTER_ELEMENT DPE_CONSENSUS DPE_NAME DPE_TYPICAL_POSITION DSE_ELEMENT_MAX_BOOST EXONUCLEASE_SPEED_FACTOR E_BOX E_BOX_CONSENSUS E_BOX_NAME E_COLI FORCE_TSS_DISABLED GC_BOX GC_BOX_CONSENSUS GC_BOX_NAME GC_ELEMENT_SCORE_BOOST HIGH_DSE_SCORE HIGH_USE_SCORE HIGH_U_CONTENT_THRESHOLD HUMAN INHIBITORY_G_RUN_PENALTY INITIATOR INITIATOR_CONSENSUS INITIATOR_NAME INR_ELEMENT_SCORE_BOOST MAX_EXON_SIZE MAX_INTRON_SIZE MAX_POLY_A_TAIL_LENGTH MAX_PROMOTER_SEARCH_DISTANCE MAX_RNA_PRIMER_LENGTH MIN_CODON_LENGTH MIN_EXON_SIZE MIN_INTRON_LENGTH_FOR_SPLICING MIN_INTRON_SIZE MIN_POLYA_SITE_STRENGTH MIN_POLY_A_DETECTION_LENGTH MIN_RNA_PRIMER_LENGTH MIN_RNA_SEQUENCE_FOR_POLYA_SEARCH MODERATE_USE_SCORE MODERATE_U_CONTENT_THRESHOLD NUCLEOTIDE_PATTERN_SYMBOLS ORGANISM_PROFILES PERFECT_DSE_SCORE PERFECT_USE_SCORE POLYA_SIGNALS POLYA_SIGNAL_OFFSET POLY_A_TAIL_PATTERN PRIMASE_SPEED_FACTOR PROMOTER_ELEMENT_COMBINATIONS PROMOTER_ELEMENT_SCORE_BOOST PROMOTER_SYNERGY_MULTIPLIER PROXIMAL_PROMOTER_ELEMENTS READING_FRAME_DIVISOR SINGLE_LETTER_CODE_ALT_CODONS_MAP SINGLE_LETTER_CODE_AMINO_ACID_DATA_MAP SPLICE_ACCEPTOR_SEQUENCES SPLICE_DONOR_SEQUENCES STANDARD_PROMOTER_ELEMENTS START_CODON STOP_CODONS STOP_CODON_UAA STOP_CODON_UAG STOP_CODON_UGA TATA_BOX TATA_BOX_CONSENSUS TATA_BOX_NAME TATA_BOX_TYPICAL_POSITION TSS_PROXIMITY_THRESHOLD USE_ELEMENT_MAX_BOOST WEAKER_ELEMENT_SCORE_BOOST

Functions

RNAtoAminoAcids add3PrimePolyATail add3PrimePolyATailAtSite add5PrimeCap buildOptimizedIntervalTree chain convertProcessedRNAToMRNA convertToDNA convertToRNA failure filterPolyadenylationSites findPolyadenylationSites findPotentialSpliceSites findPromoters findVariantsByPolypeptideLength generateAllSpliceVariants get3PrimePolyATailLength getAminoAcidByCodon getAminoAcidDataByCodon getComplementSequence getCoreSequence getDNABaseComplement getNucleotidePatternSymbolComplement getRNABaseComplement getReverseComplementSequence getStrongestPolyadenylationSite has3PrimePolyATail has5PrimeCap identifyTSS isDNA isFailure isFullyProcessed isRNA isSuccess isValidGenomicRegion isValidNucleicAcid map processAllSplicingVariants processDefaultSpliceVariant processRNA regionsOverlap remove3PrimePolyATail remove5PrimeCap replicateDNA replicateDNASimple spliceRNA spliceRNAWithVariant success transcribe unwrap unwrapOr validateExons validateNonOverlappingRegions validateNucleicAcid validateReadingFrame validateSpliceSites validateSpliceVariant

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