Finds annotations for DNA sequence in a local BLAST database.
BLAST+ is a newer version of the BLAST package and is recommended to use by the NCBI.
Element type: blast-plus
| 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
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| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Search type | Selects the type of the BLAST searches. | blastn | blast-type | string Available values are:
|
| Database path | Path to the database files. |
| db-path | string | ||
| Database name | Base name for BLAST DB files. | db-name |
| string | ||||
| Tool path | Path to the BLAST executable. | default | tool-path | string |
| Temporary directory | Directory for temporary files. | default | temp-dir | string |
| Expected value | Expectation threshold value. | 10 | e-val | numeric |
| Culling limit | If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit | 0 | max-hits | numeric |
| Annotate as | Name of the result annotations. | blast_result | result-name | string |
| Gapped alignment | Perform gapped alignment. | use | gapped-aln | boolean |
| Gap costs | Cost to create and extend a gap in an alignment. | 2 2 | gap-costs | string |
| Match scores | Reward and penalty for matching and mismatching bases. | 1 -3 | match-scores | string |
| BLAST output | Location of BLAST output file. |
| blast-output | string | |
| BLAST output type | Type of BLAST output file. | XML (-outfmt 5) |
Parameters in Workflow File
Type: blast-plus
string
Available values are:
- blastn
- blastp
- blastx
- tblastn
- tblastx
string
| type- |
| output |
| 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 |