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Parameters in GUI
Parameter | Description | Default value | |||
---|---|---|---|---|---|
Database (required) | Selects the database to search through. Available databases are blastn, blastp and cdd. | ncbi-blastn | Annotate as | Name of the result annotations. | |
Expected value | This parameter specifies the statistical significance threshold of reporting matches against the database sequences. | 10 | |||
Max hits | Maximum number of hits. | 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:
| result-name | Annotate as |
string | 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 |