Finds annotations for DNA sequence in a local BLAST database.
Element type: blast-plus
BLAST+ is used as an external tool from UGENE and it must be installed on your system. To learn more about the external tools, please, read main UGENE User Manual.
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Search type | Selects the type of the BLAST searches. | blastn | blast-type | string Available values are:
|
| Database path | Path to the database files. | db-path | string | |
| Database name | Base name for BLAST DB files. | db-name | string | |
| Tool path | Path to the BLAST executable. | default | tool-path | string |
| Temporary directory | Directory for temporary files. | default | temp-dir | string |
| Expected value | Expectation threshold value. | 10 | e-val | numeric |
| Culling limit | If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit | 0 | max-hits | numeric |
| Annotate as | Name of the result annotations. | blast_result | result-name | string |
| Gapped alignment | Perform gapped alignment. | use | gapped-aln | boolean |
| 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 |
| BLAST output | Location of BLAST output file. | blast-output | string | |
| BLAST output type | Type of BLAST output file. | XML (-outfmt 5) | type-output | 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 |