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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 =E2=80=94 path to the blastall executable. By default, the path specified in the&= nbsp;Application Settings is applied. [Str= ing, Optional, Default: =E2=80=9Cdefault=E2=80=9D]
tmpdir =E2=80=94 directory for temporary files. By d= efault, the path specified in the Application S= ettings is applied. [String, Optional, Default: =E2=80=9Cdefault= =E2=80=9D]
in =E2=80=94 semicolon-separated list of input seque= nce files. [String, Required]
dbpath =E2=80=94 path to the BLAST database files. [= String, Required]
dbname =E2=80=94 base name of the BLAST database fil= es. [String, Required]
out =E2=80=94 output Genbank file, the results of th= e search are stored as annotations. [String, Required]
name =E2=80=94 name of the annotations. [String, Opt= ional, Default: =E2=80=9Cblast result=E2=80=9D]
p =E2=80=94 type of the BLAST search. [String, Optio= nal, Default: =E2=80=9Cblastn=E2=80=9D]
The following values = are available:
e =E2=80=94 expectation value threshold. [Number, Op= tional, Default: 10]
Example:
ugene lo= cal-blast --in=3Dinput.fa --dbpath=3D. --dbname=3Dmydb --out=3Doutput.gb=20