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| 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 |
| Max 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 | Max 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
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