Task Name: local-blast
Performs a search on a local BLAST database using old version of the NCBI BLAST.
BLAST is used as an external tool and must be installed on your system.
Parameters:
toolpath — path to the blastall executable. 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