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ProteinAlphabet Class
The basic alphabet that describes symbols used in sequences of amino acids that come from codon encodings of RNA. This alphabet allows for the twenty amino acids as well as a termination and gap symbol.

The character representations come from the NCBIstdaa standard and are used in many sequence file formats. The NCBIstdaa standard has all the same characters as NCBIeaa and IUPACaa, but adds Selenocysteine, termination, and gap symbols to the latter.

The entries in this dictionary are: Symbol - Extended Symbol - Name A - Ala - Alanine C - Cys - Cysteine D - Asp - Aspartic Acid E - Glu - Glutamic Acid F - Phe - Phenylalanine G - Gly - Glycine H - His - Histidine I - Ile - Isoleucine K - Lys - Lysine L - Leu - Leucine M - Met - Methionine N - Asn - Asparagine O - Pyl - Pyrrolysine P - Pro - Proline Q - Gln - Glutamine R - Arg - Arginine S - Ser - Serine T - Thr - Threoine U - Sel - Selenocysteine V - Val - Valine W - Trp - Tryptophan Y - Tyr - Tyrosine * - Ter - Termination - - --- - Gap.

Inheritance Hierarchy

Namespace: Bio
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
Syntax
public class ProteinAlphabet : IAlphabet, 
	IEnumerable<byte>, IEnumerable

The ProteinAlphabet type exposes the following members.

Constructors
  NameDescription
Protected methodProteinAlphabet
Initializes a new instance of the ProteinAlphabet class.
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Properties
  NameDescription
Public propertyA
Gets the Alanine Amino acid.
Public propertyC
Gets the Cysteine Amino acid.
Public propertyCount
Gets count of nucleotides.
Public propertyD
Gets the Aspartic Acid.
Public propertyE
Gets the Glutamic Acid.
Public propertyF
Gets the Phenylalanine Amino acid.
Public propertyG
Gets the Glycine Amino acid.
Public propertyGap
Gets the Gap character.
Public propertyH
Gets the Histidine Amino acid.
Public propertyHasAmbiguity
Gets or sets a value indicating whether this alphabet has ambiguous characters. This alphabet does have ambiguous characters.
Public propertyHasGaps
Gets or sets a value indicating whether this alphabet has a gap character. This alphabet does have a gap character.
Public propertyHasTerminations
Gets or sets a value indicating whether this alphabet has termination characters. This alphabet does have termination characters.
Public propertyI
Gets the Isoleucine Amino acid.
Public propertyIsComplementSupported
Gets or sets a value indicating whether complement is supported or not.
Public propertyItem
Gets the byte value of item at the given index.
Public propertyK
Gets the Lysine Amino acid.
Public propertyL
Gets the Leucine Amino acid.
Public propertyM
Gets the Methionine Amino acid.
Public propertyN
Gets the Asparagine Amino acid.
Public propertyName
Gets or sets the name of this alphabet - this is always 'Protein'.
Public propertyO
Gets the Pyrrolysine Amino acid.
Public propertyP
Gets the Proline Amino acid.
Public propertyQ
Gets the Glutamine Amino acid.
Public propertyR
Gets the Arginine Amino acid.
Public propertyS
Gets the Serine Amino acid.
Public propertyT
Gets the Threoine Amino acid.
Public propertyTer
Gets the Termination character.
Public propertyU
Gets the Selenocysteine Amino acid.
Public propertyV
Gets the Valine Amino acid.
Public propertyW
Gets the Tryptophan Amino acid.
Public propertyY
Gets the Tyrosine Amino acid.
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Methods
  NameDescription
Protected methodAddAminoAcid
Adds a Amino acid to the existing amino acids.
Public methodCheckIsAmbiguous
Checks if the provided item is an ambiguous character or not
Public methodCheckIsGap
Checks if the provided item is a gap character or not
Public methodCompareSymbols
Compares two symbols.
Public methodEquals
Determines whether the specified object is equal to the current object.
(Inherited from Object.)
Protected methodFinalize
Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection.
(Inherited from Object.)
Public methodGetAmbiguousSymbols
Gets the ambigious characters present in alphabet.
Public methodGetConsensusSymbol
Find the consensus nucleotide for a set of nucleotides.
Public methodGetEnumerator
Byte array of nucleotides.
Public methodGetFriendlyName
Gets the friendly name of a given symbol.
Public methodGetHashCode
Serves as the default hash function.
(Inherited from Object.)
Public methodGetSymbolValueMap
Maps A to A and a to A that is key will contain unique values. This will be used in the IsValidSymbol method to address Scenarios like a == A, G == g etc.
Public methodGetType
Gets the Type of the current instance.
(Inherited from Object.)
Public methodGetValidSymbols
Gets the valid symbol.
Protected methodMapAmbiguousAminoAcid
Maps the ambiguous amino acids to the amino acids it represents. For example ambiguous amino acids M represents the basic nucleotides A or C.
Protected methodMemberwiseClone
Creates a shallow copy of the current Object.
(Inherited from Object.)
Public methodToString
Converts the Protein Alphabets to string.
(Overrides ObjectToString.)
Public methodTryGetAmbiguousSymbol
Gets the Ambiguous symbol.
Public methodTryGetBasicSymbols
Gets the Basic symbol.
Public methodTryGetComplementSymbol(Byte, Byte)
Gets the complement of the symbol.
Public methodTryGetComplementSymbol(Byte, Byte)
This method tries to get the complements for specified symbols.
Public methodTryGetDefaultGapSymbol
Gets the default Gap symbol.
Public methodTryGetDefaultTerminationSymbol
Gets the default Termination symbol.
Public methodTryGetGapSymbols
Gets the Gap symbol.
Public methodTryGetTerminationSymbols
Gets the Termination symbol.
Public methodValidateSequence
Validates if all symbols provided are Protein symbols or not.
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Fields
  NameDescription
Public fieldStatic memberInstance
Instance of this class.
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Extension Methods
  NameDescription
Public Extension MethodAppendByte(Byte)Overloaded.
Yield an Enumeration of the list with the item appended to the end
(Defined by IEnumerableExtensions.)
Public Extension MethodAppendByte(IEnumerableByte)Overloaded.
Yield a concatenation of the two Enumerable lists
(Defined by IEnumerableExtensions.)
Public Extension MethodCheckIsAmbiguous
Checks if the provided item is an ambiguous character or not
(Defined by AlphabetExtensions.)
Public Extension MethodCheckIsGap
Checks if the provided item is a gap character or not
(Defined by AlphabetExtensions.)
Public Extension MethodCheckIsTermination(Byte)Overloaded.
This returns true/false if the given symbol value is considered a termination value in the alphabet.
(Defined by AlphabetExtensions.)
Public Extension MethodCheckIsTermination(Char)Overloaded.
This returns true/false if the given symbol value is considered a termination value in the alphabet.
(Defined by AlphabetExtensions.)
Public Extension MethodElementAtByte
Returns the element at a specified index in a sequence.
(Defined by IEnumerableExtensions.)
Public Extension MethodForEachByte(ActionByte)Overloaded.
Calls an action on each element of a sequence. The action takes one argument: an element. It has no return value.
(Defined by IEnumerableExtensions.)
Public Extension MethodForEachByte(ActionByte, Int32)Overloaded.
Calls an action on each element of a sequence. The action takes two arguments: an element and the index of the element. It has no return value.
(Defined by IEnumerableExtensions.)
Public Extension MethodGetFriendlyName
Gets the friendly name of a given symbol.
(Defined by AlphabetExtensions.)
Public Extension MethodGetMummerAlphabet
Find corresponding mummer alphabet which supports the concatenation symbol using an existing alphabet
(Defined by MummerAlphabetExtensions.)
Public Extension MethodShuffleByte
Shuffles the elements of a sequence.
(Defined by IEnumerableExtensions.)
Public Extension MethodStringJoinOverloaded.
Creates a string from a sequence of elements. No delimiter is used.
(Defined by IEnumerableExtensions.)
Public Extension MethodStringJoin(String)Overloaded.
Creates a delimited string from a sequence of elements.
(Defined by IEnumerableExtensions.)
Public Extension MethodStringJoin(String, Int32, String)Overloaded.
Creates a delimited string from a sequence of elements. At most maxLength elements will be used and "..." shows that more elements were in the list.
(Defined by IEnumerableExtensions.)
Public Extension MethodSubSequenceByte
Take the items from a sequence starting with item # start (index 0) and contining for count items.
(Defined by IEnumerableExtensions.)
Public Extension MethodToHashSetByteOverloaded.
Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created.
(Defined by IEnumerableExtensions.)
Public Extension MethodToHashSetByte(IEqualityComparerByte)Overloaded.
Creates a HashSet from a sequence. If the sequence is already a HashSet, a new HashSet is still created.
(Defined by IEnumerableExtensions.)
Public Extension MethodToQueueByte
Creates a Queue from a sequence. If the sequence is already a Queue, a new Queue is still created.
(Defined by IEnumerableExtensions.)
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See Also

Reference