Task Name: local-blast+
Performs a search on a local BLAST database using BLAST+.
BLAST+ is used as an external tool and must be installed on your system.
Parameters:
toolpath — path to an appropriate BLAST executable (e.g. blastn, blastp, etc.). By default, the path specified in the Application Settings is applied. [String, Optional, Default: “default”]
tmpdir — directory for temporary files. By default, the path specified in the Application Settings is applied. [String, Optional, Default: “default”]
in — semicolon-separated list of input sequence files. [String, Required]
dbpath — path to the BLAST database files. [String, Required]
dbname — base name of the BLAST+ database files. [String, Required]
out — output Genbank file, the results of the search are stored as annotations. [String, Required]
name — name of the annotations. [String, Optional, Default: “blast result”]
p — type of the BLAST search. [String, Optional, Default: “blastn”]
The following values are available:
- blastn
- blastp
- blastx
- tblastn
- tblastx
e — expectation value threshold. [Number, Optional, Default: 10]
Example:
ugene local-blast+ --in=input.fa --dbpath=. --dbname=mydb --out=output.gb