BLAST Help

Other option

Please input a parameter directly to perform a detailed setup. 

The option which can be specified is as follows. 
Please place "-" (minus) before an option and divide each parameter in a space. 
Examplej -G 2 -E 1 -q -2

e => Expectation vaule (E) default=10.0 

m => alignment view default=0 0 = pairwise, 1 = master-slave showing identities, 2 = master-slave no identities, 3 = flat master-slave, show identities, 4 = flat master-slave, no identities, 5 = master-slave no identities and blunt ends, 6 = flat master-slave, no identities and blunt ends 

F => Filter query sequence default=T (DUST with blastn, SEG with others) 

G => Cost to open a gap default=0 (zero invokes default behavior) 

E => Cost to extend a gap default=0 (zero invokes default behavior) 

X => X dropoff value for gapped alignment (in bits) default=0 (zero invokes default behavior) 

I => Show GI's in deflines default=F 

q => Penalty for a nucleotide mismatch (blastn only) default=-3 

r => Reward for a nucleotide match (blastn only) default=1 

v => Number of one-line descriptions (V) default=500 

b => Number of alignments to show (B) default=250 

f => Threshold for extending hits, default if zero default=0 

g => Perfom gapped alignment (NA with tblastx) default=T 

Q => Query Genetic code to use default=1 

D => DB Genetic code (for tblast[nx] only) default=1 

a => Number of processors to use default=1 

O => SeqAlign file Optional 

J => Believe the query defline default=F 

M => Matrix default=BLOSUM62 

W => Word size, default if zero default=0 

z => Effective length of the database default=0 (use zero for the real size)