Finds annotations for the supplied DNA sequence in local BLAST database.
Warning |
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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 |
Max hits | 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 |
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 hits | numeric |
result-name | Annotate as | string |
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 |