Finds annotations for the supplied DNA sequence in the NCBI remote database.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Database | Selects the database to search through. Available databases are blastn, blastp and cdd. | ncbi-blastn |
| Expected value | This parameter specifies the statistical significance threshold of reporting matches against the database sequences. | 10 |
| Max hits | Maximum number of hits. The maximum available number is 5000. | 10 |
| Short sequence | Optimizes search for short sequences. | False |
| Entrez query | Enter an Entrez query to limit search. | |
| Annotate as | Name of the result annotations. | |
| BLAST output | Location of the BLAST output file. This parameter insignificant for cdd search. | |
| Gap costs | Cost to create and extend a gap in an alignment. | 2 2 |
| Match scores | Reward and penalty for matching and mismatching bases. | 1 -3 |
Parameters in Workflow File
Type: blast-ncbi
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| db | Database | string Available values are:
|
| e-val | Expected value | string |
| max-hits | Max hits | numeric |
| short-sequence | Short sequence | boolean |
| entrez-query | Entrez query | string |
| result-name | Annotate as | string |
| blast-output | BLAST output | string |
| gap-costs | Gap costs | string |
| match-scores | Match scores | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input sequence
Name in Workflow File: in-sequence
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |
And 1 output port:
Name in GUI: Annotations
Name in Workflow File: out-annotations
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Set of annotations | annotations | annotation-table |