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Benchling APIRna Sequence

Update RnaSequence

Update an RNA sequence. The id path parameter identifies the RNA sequence to update.

Sequence specification

To replace the sequence, provide exactly one of the following. Omit all sequence fields to keep the existing sequence.

  • bases — plain nucleotide sequence
  • helm — HELM notation (requires the modified nucleotides feature to be enabled)
  • customNotation with customNotationId — vendor-specific notation (requires custom syntaxes to be enabled; both fields must be set together)

Updating bases

When replacing bases, include every sequence feature collection that already exists on the sequence: annotations, translations, primers, and parts. Provide the updated values or an empty array ([]) to clear a collection. Omitting a key that has existing data returns 400.

Chemical modifications

When switching from HELM or custom notation to plain bases on a sequence with chemical modifications, include an empty helm or customNotation string to clear the existing modifications. Updating bases alone returns 400.

Authentication

AuthorizationBearer

Bearer authentication of the form Bearer <token>, where token is your auth token.

Path parameters

rna_sequence_idstringRequired
ID of the RnaSequence.

Request

This endpoint expects an object.
aliaseslist of stringsOptional
Array of aliases
allowCustomFieldDeletionbooleanOptional
When true, custom fields present on the entity but omitted from the update payload will be deleted. When false or omitted, omitting existing custom fields is an error. Defaults to false.
annotationslist of objectsOptional
Annotations on the RNA sequence, not including translations or primers. Annotations on parts are not included.
archiveReasonstringOptional
archivedbooleanOptional
authorIdslist of stringsOptional
basesstringOptional

Bases of the RNA sequence. Mutually exclusive with helm and customNotation.

customFieldsmap from strings to objectsOptional
Custom fields set on the RNA sequence.
customNotationstring or nullOptional

Sequence in a vendor-specific custom notation syntax. Requires custom syntaxes to be enabled. When customNotation is set, customNotationId is required. Mutually exclusive with bases and helm.

customNotationIdstring or nullOptional

ID of the custom notation syntax used to interpret customNotation. When customNotation is set, customNotationId is required; omit both when using bases or helm.

entityRegistryIdstringOptional

Registry ID to assign to the entity. When registering, specifying this value sets the registry ID of the entity. When already registered, specifying this value updates the entity’s registry ID. If set, naming_strategy must be unspecified.

folderIdstringOptional
helmstringOptional

HELM notation for the RNA sequence and chemical modifications. Requires the modified nucleotides feature to be enabled. Mutually exclusive with bases and customNotation.

namestringOptional
Name of the item.
namingStrategyenumOptional

Strategy to use for labeling the item in the registry if registering. If one is specified, the entity_registry_id must be unspecified.

partslist of objectsOptional
Part features linking regions of this sequence to other RNA sequences.
primerslist of objectsOptional
Primer bind features on the RNA sequence. Primers on parts are not included.
registryIdstring or nullOptional
A not null value means the entity should be registered. A null value means it should be unregistered. If not null, the value must match the registry of the item's schema.
schemaFieldsmap from strings to objectsOptional
schemaIdstringOptional
translationslist of objectsOptional
Translation annotations present on the RNA sequence. Translations may be one region or split across multiple regions. Translations on parts are not included.

Response

OK
__typenamestringOptional
authorsstring or nullOptionalformat: "uri"
creatorobject or nullOptional
schemaFieldslist of objects or nullOptional
aliaseslist of strings or nullOptional
Array of aliases
annotationsstringOptionalformat: "uri"
Annotations on the RNA sequence, not including translations or primers. Annotations on parts are not included.
archiveReasonstring or nullOptional
archivedbooleanOptional
basesstringOptional
Bases of the RNA sequence.
canonicalHelmstringOptional
Normalized HELM notation for this RNA sequence.
createdAtstring or nullOptional
customFieldslist of objects or nullOptional
Custom fields set on the RNA sequence.
entityRegistryIdstring or nullOptional

The registry-assigned identifier for this item (e.g. its registry ID shown in the UI), present only once the item has been registered. Null if the item is not registered.

folderobject or nullOptional
idstringOptional
modifiedAtstring or nullOptional
modifiedNucleotidesstringOptionalformat: "uri"
Modifications applied to this RNA sequence.
namestringOptional
Name of the item.
nucleotideAlignmentsstringOptionalformat: "uri"

Nucleotide alignments that use this sequence as the reference sequence. For template alignments, this is the template sequence; for consensus alignments, this is the derived consensus sequence.

partsstringOptionalformat: "uri"
Part features linking regions of this sequence to other RNA sequences.
primersstringOptionalformat: "uri"
Primer bind features on the RNA sequence. Primers on parts are not included.
projectobject or nullOptional
registrationOriginobject or nullOptional

Provenance of this item’s registration — where and when it was registered. Null if unregistered.

registryobject or nullOptional
The Registry this item belongs to, if registered. Null if unregistered.
schemaobject or nullOptional

Use typedSchema instead, which returns the per-type schema.

translationsstringOptionalformat: "uri"
Translation annotations present on the RNA sequence. Translations may be one region or split across multiple regions. Translations on parts are not included.
typedSchemaobject or nullOptional

Errors

400
Rna Sequence Update Request Bad Request Error
403
Rna Sequence Update Request Forbidden Error
404
Rna Sequence Update Request Not Found Error
409
Rna Sequence Update Request Conflict Error
429
Rna Sequence Update Request Too Many Requests Error
500
Rna Sequence Update Request Internal Server Error