Finds annotations for the supplied DNA sequence in local BLAST database.
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 in GUI
| Parameter | Description | Default value |
|---|---|---|
| Search type | Selects the type of the BLAST searches. | blastn |
| Database path | Path to the database files. | |
| Database name | Base name for BLAST DB files. | |
| Tool path | Path to the BLAST executable. | default |
| Temporary directory | Directory for temporary files. | default |
| Expected value | Expectation threshold value. | 10 |
| Best hits limit | Specifies the number of best hits from a region of the query to keep. 0 turns it off. If used, 100 is recommended. | 0 |
| Annotate as | Name of the result annotations. | blast_result |
| Gapped alignment | Perform gapped alignment. | use |
| 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 |
| BLAST output | Location of BLAST output file. | |
| BLAST output type | Type of BLAST output file. | XML (-m 7) |
Parameters in Workflow File
Type: blast
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| blast-type | Search type | string Available values are:
|
| db-path | Database path | string |
| db-name | Database name | string |
| tool-path | Tool path | string |
| temp-dir | Temporary directory | string |
| e-val | Expected value | numeric |
| max-hits | Best hits limit | numeric |
| result-name | Annotate as | string |
| gapped-aln | Gapped alignment | boolean |
| gap-costs | Gap costs | string |
| match-scores | Match scores | string |
| blast-output | BLAST output | string |
| type-output | BLAST output type | 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 |