Read Sequence from Remote Database Element
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 to the selected database.
The element outputs message(s) with the sequence and annotations data.
Element type: fetch-sequence
Parameters
| Parameter | Description | Default Value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Resource IDs (required) | Semicolon-separated list of resource IDs in the database. | resource-id | string | |
| Database (required) | Name of the database to read from. | NCBI Genbank (DNA sequence) | database | string |
| 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 file to directory | Directory to store a file loaded from the database. | default | save-dir | string |
| Read resource ID(s) from source | The source to read resource IDs from the list or a local file. | List of TDs | ids-source | string |
Input/Output Ports
The element has 1 output port:
| Name in GUI | Name in Workflow File | Type |
|---|---|---|
| Sequence | out-sequence | sequence |
| Set of annotations | annotations | annotation-table |