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BLAST+ is a newer version of the BLAST package and is recommended to use by the NCBI.
| Warning |
|---|
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 | ||
|---|---|---|---|---|
| Database name (required) | Base name for BLAST DB files. | |||
| 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 (required) | Path to a the BLAST + executableexecutable. | default | ||
| Temporary directory | Directory for temporary files. | default | ||
| Search type (required) | Selects the type of BLAST searches. | blastnExpected value | Expectation threshold value. | 10 |
| Annotate as | Name of the result annotations. | misc_feature | ||
| Expected value | Expectation threshold value. | 10 | ||
| Temporary directory (required) | Directory for temporary files. | defaultblast_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 (-outfmt 5) |
Parameters in Workflow File
Type: blast-plus
| Parameter | Parameter in the GUI | Type | ||
|---|---|---|---|---|
| blast-type | Search type | string Available values are:
| ||
| db- | namepath | Database | namepath | string |
| db-pathname | Database pathname | string | ||
| tool-path | Tool path | string | ||
| blasttemp-typedirSearch type | Temporary directory | string Available values are: | ||
| e-val | Expected value | numeric | ||
| result-name | Annotate as | string | ||
| e-val | Expected value | numeric | ||
| temp-dir | Temporary directorygapped-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 Schema 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 |