SequenceQ -- Checks if a sequence is matching the given polymer type, such as DNA, RNA, or peptide.

ValidSequenceQ -- Checks if a sequence is a valid DNA, RNA, or peptide sequence.

SequenceLength -- Computes the number of monomers in the provided polymer sequence.

PolymerType -- Determines the possible polymer type that the provided sequence could be composed of.

DNAQ -- Checks if a sequence is a valid DNA sequence.

RNAQ -- Checks if a sequence is a valid RNA sequence.

PeptideQ -- Checks if a sequence is a valid peptide sequence.

PNAQ -- Checks if a sequence is a valid peptide nucleic acid (PNA) sequence.

GammaRightPNAQ -- Checks if a sequence is a valid right-handed gamma-modified PNA sequence.

GammaLeftPNAQ -- Checks if a sequence is a valid left-handed gamma-modified PNA sequence.

ModificationQ -- Checks if a sequence is a sequence of modifications.

SameSequenceQ -- Checks that for the provided list of sequences, if each of them are or could represent the same sequence.

ReverseSequenceQ -- Checks if two sequences are the reverse sequence of each other.

ComplementSequenceQ -- Checks if two sequences are the Watson-Crick complement of each other.

ReverseComplementSequenceQ -- Checks if two sequences are the reverse complement of each other.

SequencePalindromeQ -- Checks if a sequence is palindromic, which means that the sequence is its own reverse complement.

SequenceFirst -- Returns the first monomer of the provided sequence.

SequenceLast -- Returns the last monomer of the provided sequence.

SequenceMost -- Returns all but the last monomer of the provided sequence.

SequenceRest -- Returns all but the first monomer of the provided sequence.

SequenceTake -- Returns the specified part of the provided sequence.

SequenceDrop -- Returns a sequence with the specified part dropped from the provided sequence.

SequenceJoin -- Joins the provided sequences together into a single sequence.

SequenceRotateLeft -- Moves the first n monomers from the front (left hand side) of the sequence to the rear (right hand side) of sequence.

SequenceRotateRight -- Moves the last n monomers from the rear (right hand side) of the sequence to the front (left hand side) of sequence.

ExplicitlyTypedQ -- Checks if a sequence is explicitly typed.

ExplicitlyType -- Removes or adds the explicit polymer type to a sequence.

UnTypeSequence -- Removes the polymer type and motif from a sequence.

Monomers -- Splits a sequence into a list of its composite monomers.

Dimers -- Splits a sequence into a list of its composite overlapping dimers in order of the sequence.

AllSequences -- Returns a list of all possible sequences of the requested length.

RandomSequence -- Returns a random sequence of the requested length.

AllPalindromes -- Returns all palindromic sequences of the requested length.

ReverseSequence -- Returns the reverse sequence of the provided sequence.

ComplementSequence -- Returns the complement sequence of the provided sequence.

ReverseComplementSequence -- Returns the reverse complement of the provided sequence.

ToDNA -- Converts a sequence into its equivalent DNA sequence.

ToRNA -- Converts a sequence into its equivalent RNA sequence.

ToLRNA -- Converts a sequence into its equivalent L-form RNA sequence.

ToPeptide -- Converts a protein sequence in the single letter amino acid form into an explicitly typed Peptide in the triple letter abbreviation form.

ToSequence -- Returns a list of sequences in the strand or in the motifs.

GenerateSequence -- Generates an optimal sequence with degenerate bases filled in, given certain parameters and specific sequences.

UploadModification -- Creates a new Constellation object referring to a specified chemical modification.

FractionAT -- Computes the fraction of the provided DNA/PNA sequence that is composed of As or Ts.

FractionAU -- Computes the fraction of the provided RNA sequence that is composed of As or Us.

FractionGC -- Computes the fraction of the provided DNA/RNA/PNA sequence that is composed of As or Us.

FractionMono -- Computes the fraction of the provided sequence that is composed of members of the provided list of monomers.

FractionPurine -- Computes the fraction of the provided DNA/RNA/PNA sequence that is composed of purines (As and Gs).

FractionPyrimidine -- Computes the fraction of the provided DNA/RNA/PNA sequence that is composed of purines (Cs, Ts, and Us).

EmeraldSubsequences -- Splits the provides sequence into a list of overlapping subsequences of length n.

FoldsQ -- Checks if a fold of a specific length exists anywhere in the provided sequence.

NumberOfFolds -- Computes the total number of overlapping subsequences of a specific length that could fold from the provided sequence.

FoldingSequences -- Returns a list of subsequences of a specific length from the provided sequence that could potentially fold.

FoldingMatrix -- Returns a matrix describing if the overlapping subsequences of a specific length from start to finish of the provided sequence could fold onto each other.

RepeatsQ -- Checks if a repeated subsequence of a specific length exists anywhere in the provided sequence.

NumberOfRepeats -- Computes the total number of overlapping subsequences of a specific length that are repeated from the provided sequence.

RepeatingSequences -- Returns a list of subsequences of a specific length that are repeated from the provided sequence.

RepeatingMatrix -- Returns a matrix describing if the overlapping subsequences of a specific length from start to finish the provided sequence are repeated.

MotifForm -- Looks for anything in Structure form from the provided input and renders them as graph images at the motif level.

ValidMotifQ -- Checks if a sequence is a valid motif, which mean an explicitly typed sequence.

MotifSequence -- Returns the sequence of the provided motif.

MotifPolymer -- Returns the polymer type of the provided motif.

MotifLabel -- Returns the label of the provided motif.

NameMotifs -- Names any unnamed motifs with a unique string in the provided structure, strand, or sequence.

DefineMotifs -- Applies the replacement rules to all motifs to replace them with specified sequences.

ExactMass -- Computes the most probable exact mass of a given molecule.

MolecularWeight -- Computes the molecular weight of a molecule, oligomer, or the average molecular weight of a polymer.

ExtinctionCoefficient -- Computes the extinction coefficient at 260 nm of the provided sequence.

Hyperchromicity260 -- Computes the hyperchromicity correction of the provided sequence.

ValidPolymerQ -- Checks if the info contained in the provided input is of correct construction.

DNAPhosphoramiditeMolecularWeights -- Returns a list of the molecular weights (in grams/mole) of the DNA phosphoramidite monomer as rules.

PNAMolecularWeights -- Returns a list of the molecular weights for PNA reagents.

ModifierPhosphoramiditeMolecularWeights -- Returns a list of the molecular weights (in grams/mole) of the modifier phosphoramidite monomer as rules.

Strand -- Represents a strand with one or more motifs.

StrandQ -- Checks if the provided input is a properly formatted strand (each sequence is a properly formatted sequence of the given polymer type).

ValidStrandQ -- Checks if the provided input is a properly formatted strand (each sequence is a properly formatted sequence of the given polymer type).

StrandLength -- Returns the length of the strand as defined by the total number of monomers.

StrandFirst -- Returns a strand containing only the first monomer of the provided strand.

StrandLast -- Returns a strand containing only the last monomer of the provided strand.

StrandRest -- Returns a strand with of all but the first monomer of the provided strand.

StrandMost -- Returns a strand with of all but the last monomer of the provided strand.

StrandTake -- Returns the specified part of the provided strand.

StrandDrop -- Returns a strand with the specified part dropped from the provided strand.

StrandJoin -- Joins the provided strands together into a single strand.

StrandFlatten -- Takes a strand and joins consecutive stretches of like polymer types into single polymers.

Truncate -- Returns a list of strands by removing a specific number of monomers from the provided strand and replacing them with a single cap monomer.

ToStrand -- Returns a single strand or a list of strands containing from the provided sequences or structures.

ParseStrand -- Returns the motif name, reverse complement status, sequence, and polymer type of the provided strand.

Structure -- Represents a structure with one or more strands and zero or more bonds.

StructureQ -- Checks if the provided input is a properly formatted structure.

StructureFaces -- Returns a list of faces for the structure, which contains the corresponding loop type and start/end indices in the original structure.

StructureJoin -- Joins the provided structures together into a single structure.

StructureSort -- Sorts a structure into canonical form using alphabet and graph topology.

StructureTake -- Returns the specified part of the provided structure.

SplitStructure -- Splits a structure into separate structures that share no bonds between strands.

ToStructure -- Returns a single structure containing a single strand or multiple strands from the provided sequences or strands.

Hybridize -- Joins reverse-complementary sequences until no more are available.

Pairing -- Returns all possible pairings of two provided sequences, strands, or structures.

NumberOfBonds -- Computes the number of bonds in the provide structure.

StructureForm -- Looks for anything in Structure form from the provided input and renders them as graph images at the nucleotide level.

State -- Represents a state containing species and their concentrations.

StateQ -- Checks if the provided input is a properly formatted state.

ToState -- Converts a list of rules, relating species name with concentration, to a properly formatted state.

StateFirst -- Returns the first name and concentration pair of the provided state.

StateLast -- Returns the last name and concentration pair of the provided state.

StateRest -- Returns all but the first name and concentration pair of the provided state.

StateMost -- Returns all but the last name and concentration pair of the provided state.

Reaction -- Represents either an irreversible or a reversible chemical reaction.

ReactionQ -- Checks that if the provided nucleic acid reaction is properly formatted.

SplitReaction -- Splits a reversible reaction into forward and reverse reactions.

ToReactionMechanism -- Constructs a properly formatted ReactionMechanism from the provided reactions and rates.

ClassifyReaction -- Returns the classical type of a nucleic acid secondary structure transformation based on the provided nucleic acid reactants and products.

KineticRates -- Returns an estimated kinetic rate parameterized from literature precedence for the nucleic acid reaction with a classified reaction type.

ReactionMechanism -- Represents a ReactionMechanism containing a set of reactions.

ReactionMechanismQ -- Checks if the provided input is a properly formatted mechanism.

MechanismFirst -- Returns the first reaction from the provided mechanism.

MechanismLast -- Returns the last reaction from the provided mechanism.

MechanismRest -- Returns all but the first reaction from the provided mechanism.

MechanismMost -- Returns all but the last reaction from the provided mechanism.

MechanismJoin -- Joins two or more mechanisms together and deletes redundant reactions.

SpeciesList -- Returns a list of unique species present in the provided reactions.

Trajectory -- Represents a trajectory describing the behavior of reactions.

ToTrajectory -- Transforms a list of data points and time points into a properly formatted Trajectory.

PlotTrajectory -- Plots the concentration of all species in the provided trajectory against time.