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Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Database | Selects the database to search through. Available databases are blastn, blastp and cdd. | ncbi-blastn |
| Expected value | This parameter specifies the statistical significance threshold of reporting matches against the database sequences. | 10 |
| Max hits | Maximum number of hits. The maximum available number is 5000. | 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
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