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  • Read Sequence from Remote Database Element
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Download sequence(s) with the specified ID(s) from one of the remote databases: NCBI, Ensembl, PDB, etc.

The sequences are downloaded with the associated annotations in a file format, specific for the selected database.

The element outputs message(s) with the sequence and annotations data.

Parameters in GUI


ParameterDescriptionDefault value
Resource IDs (required)Semicolon-separated list of resource IDs in the database. 
Database (required)Name of the database to read from.NCBI Genbank (DNA sequence)
Save file to directoryDirectory to store a file loaded from the database.default
Read resource ID(s) from sourceThe source to read resource IDs from the list or a local file.List of TDs

Parameters in Workflow File

Type: fetch-sequence

ParameterParameter in the GUIType
resource-idResource IDsstring


Available values are:

  • ncbi-dna (NCBI GenBank (DNA sequence))
  • ncbi-protein (NCBI protein sequence database)
  • pdb (PDB)
  • swiss-plot (SWISS-PROT)
  • uniprot-swiss-prot (UniProtKB/Swiss-Prot)
  • uniprot-trembl (UniProtKB/TrEMBL)
save-dirSave file to directorystring
ids-sourceRead resource ID(s) from sourcestring

Input/Output Ports

The element has 1 output port:

Name in GUI: Sequence

Name in Workflow File: out-sequence


Slot In GUISlot in Workflow FileType
Set of annotationsannotationsannotation-table
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