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.
Examplej -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)