BioSequenceType

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Alphabets and relationships between letters that allow strings to represent biological sequences.

Entity["BioSequenceType",name] or

represents an entity of type "BioSequenceType".

[prop]

gives the value of a specified property.

[{propi,…}]

gives the value of a list of properties.

Sample Entities

  • …

Properties

  • AdditionalBondTypesadditional bond types
    AllowedBondingRulesallowed bonding rules
    Alphabetalphabet
    AlphabetRulesalphabet rules
    AlternateEncodingRulesalternate encoding rules
    BondTypesall associated bond types
    Captioncaption
    CircularQcircular
    ComplementLetterRulescomplement letter rules
    DegenerateAlphabetdegenerate alphabet
    DegenerateLetterRulesdegenerate letter rules
    EntityTypeListentity type list
    FullAlphabetall letters
    Namename
    PrimaryStructureBondTypeprimary structure bond type

Details

  • "BioSequenceType" entities include the standardized alphabets most commonly used in biological sequence processing.
  • Some properties are available for the "BioSequenceType" entity type as a whole and can be given using the form EntityValue["BioSequenceType",property]. Such properties include:
  • "Properties"the list of available properties
    "PropertyCanonicalNames"the standard names of available properties
    "SampleEntities"a sample list of available entities (typically of length 10)
    "SampleEntityClasses"a sample list of available entity classes (typically of length 10)
    "EntityCount"number of entities available
    "Entities"the list of available entities
    "EntityCanonicalNames"the standard names of available entities
    "EntityClasses"the list of available entity classes
    "EntityClassCanonicalNames"the standard names of available entity classes
    "PropertyClasses"the list of available property classes
    "PropertyClassCanonicalNames"the standard names of available property classes
    "PropertyCount"number of properties available
  • The following annotations can be used in the third argument of EntityValue["BioSequenceType",property,annotation]:
  • "Source"source information for the property
    "Date"the date associated with the entity-property value (if any)
    "EntityAssociation"an association of entities and entity-property values
    "PropertyAssociation"an association of properties and entity-property values
    "EntityPropertyAssociation"an association in which the specified entities are keys, and values are a nested association of properties and entity-property values
    "PropertyEntityAssociation"an association in which the specified properties are keys, and values are a nested association of entities and entity-property values
    "Dataset"a dataset in which the specified entities are keys, and values are an association of property names and entity-property values
  • The following annotations can be used in the second argument of EntityValue[property,annotation]:
  • "Qualifiers"the list of possible qualifiers for the property
    "QualifierValues"the list of possible values that can be given to each qualifier
    "DefaultQualifierValues"the list of default values for the property's qualifiers
    "Description"a brief textual description of the property
    "Definition"a detailed textual definition of the property
    "PhysicalQuantity"the physical quantity associated with the entity-property value
    "Unit"the unit associated with the entity-property value
  • A qualifier value of Automatic indicates that an applicable format of values can be used; e.g. for the "Date" qualifier, this includes a proper date or date span.

Examples

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Basic Examples  (3)

Use for entity discovery:

Find a property value for an entity:

Retrieve a dataset of all available properties for an entity:

Applications  (2)

"BioSequenceType" entities can be used to construct BioSequence expressions:

The type of any BioSequence object is a BioSequenceType entity:

Neat Examples  (1)

Build a dataset of the interpretation for each letter allowed in a RNA sequence: