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 |
Database | Select the database to search through. | |
Expected value | This parameter specifies the statistical significance threshold of reporting matches against the database sequences. | 10 |
Results limit | The maximum number of results. | 10 |
Megablast | Use megablast. | False |
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:
|
db | Database | string |
e-val | Expected value | string |
hits | Results limit | numeric |
megablast | Megablast | boolean |
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 |