CD-Search Element
This tool identifies conserved domains in protein sequences. If the conserved domains database is downloaded, the search can be performed locally. Otherwise, the search can be submitted to the NCBI for remote execution.
Element type: cd-search
Parameters
| Parameter | Description | Default Value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Annotate as | The name of the result annotations marking found conserved domains. | CDD result | result-name | string |
| Database | CD-Search is offered with the following databases: • CDD – superset including curated and imported domains • Pfam – curated seed alignments • SMART – domain alignments, some limitations • TIGRFAM – curated HMM alignments • COG – orthologous protein families • KOG – eukaryotic orthologs • Prk – protein kinases | CDD | db-name | string |
| Database directory | Specifies the path to the local copy of the database used for local search. | db-path | string | |
| Local search | If True, performs the search locally. If False, submits the query to NCBI for remote execution. | True | local-search | boolean |
| Expect value | Modifies the E-value threshold for filtering results. A typical cutoff is 0.01. Results with E-values > 1 are usually considered unreliable. | e-val | numeric |
Input/Output Ports
| Port Name (GUI) | Workflow File Name | Slots |
|---|---|---|
| Input sequence | in-sequence | Sequence → sequence (sequence) |
| Annotations | out-annotations | Set of annotations → annotations (annotation-table) |