BEbenchling
RNA 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.

patch/api/v3/rna-sequence/{rna_sequence_id}

Request

  • Base URL
    https://{tenant_name}.benchling.com
  • Auth
    HTTP bearer

Path parameters

rna_sequence_idstring required

ID of the RnaSequence.

Request body

aliasesstring[]

Array of aliases

allowCustomFieldDeletionboolean

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.

archiveReasonstring

Why it is being archived. Required when archived is true, and not allowed when unarchiving.

archivedboolean

Set to true to archive or false to unarchive it. Archiving requires archiveReason.

authorIdsstring[]
basesstring

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

customFieldsobject

Custom fields set on the RNA sequence.

customNotationstring nullable

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 nullable

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

entityRegistryIdstring

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.

folderIdstring
helmstring

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

namestring

Name of the item.

namingStrategy'NEW_IDS' | 'IDS_FROM_NAMES' | 'DELETE_NAMES' | 'SET_FROM_NAME_PARTS' | 'REPLACE_NAMES_FROM_PARTS' | 'KEEP_NAMES' | 'REPLACE_ID_AND_NAME_FROM_PARTS'

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

registryIdstring nullable

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.

schemaFieldsobject
schemaIdstring

Response

OK

__typenamestring
aliasesstring[] nullable

Array of aliases

annotationsstring uri

Annotations on the RNA sequence, not including translations or primers. Annotations on parts are not included.

archiveReasonstring nullable
archivedboolean
basesstring

Bases of the RNA sequence.

canonicalHelmstring

Normalized HELM notation for this RNA sequence.

createdAtstring datetime nullable
entityRegistryIdstring nullable

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.

idstring
modifiedAtstring datetime nullable
modifiedNucleotidesstring uri

Modifications applied to this RNA sequence.

namestring

Name of the item.

nucleotideAlignmentsstring 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.

partsstring uri

Part features linking regions of this sequence to other RNA sequences.

primersstring uri

Primer bind features on the RNA sequence. Primers on parts are not included.

translationsstring uri

Translation annotations present on the RNA sequence. Translations may be one region or split across multiple regions. Translations on parts are not included.

authorsstring uri nullable

Changes

No recorded changes to this operation across all 1 revision of this API.