Finds annotations for the supplied DNA sequence in the NCBI remote database.
Element type: blast
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Database | Selects the database to search through. Available databases are blastn, blastp and cdd. | ncbi-blastn | db | string Available values are:
|
| Database | Select the database to search through. | db | string | |
| Expected value | This parameter specifies the statistical significance threshold of reporting matches against the database sequences. | 10 | e-val | string |
| Results limit | The maximum number of results. | 10 | hits | numeric |
| Megablast | Use megablast. | False | megablast | boolean |
| Short sequence | Optimizes search for short sequences. | False | short-sequence | boolean |
| Entrez query | Enter an Entrez query to limit search. | entrez-query | string | |
| Annotate as | Name of the result annotations. | result-name | string | |
| BLAST output | Location of the BLAST output file. This parameter insignificant for cdd search. | blast-output | string | |
| Gap costs | Cost to create and extend a gap in an alignment. | 2 2 | gap-costs | string |
| Match scores | Reward and penalty for matching and mismatching bases. | 1 -3 | 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 |