|
-a
|
SeqAnnot output file.
|
[File Out]
|
|
|
-d
|
Theoretical database size (0 is real size).
|
[Integer]
|
0
|
|
-e
|
Expectation value (E).
|
[Real]
|
10.0
|
|
-g
|
Gapped.
|
[T/F]
|
T
|
|
-i
|
First sequence.
|
[File In]
|
|
|
-j
|
Second sequence.
|
[File In]
|
|
|
-m
|
Use MegaBLAST for search.
|
[T/F]
|
F
|
|
-o
|
Alignment output file.
|
[File Out]
|
stdout
|
|
-p
|
Program name: blastp,
blastn, blastx,
tblastn, tblastx. For
blastx, the first sequence should be nucleotide;
for tblastn, the 2nd sequence sequence should be
nucleotide.
|
[String]
|
|
|
-q
|
Penalty for a nucleotide mismatch (blastn only).
|
[Integer]
|
-3
|
|
-r
|
Reward for a nucleotide match (blastn only).
|
[Integer]
|
1
|
|
-t
|
Length of the largest intron allowed in tblastn
for linking HSPs.
|
[Integer]
|
0
|
|
-A
|
Input sequences in the form of <accession.version>.
|
[T/F]
|
F
|
|
-D
|
Output format: 0 = traditional; 1 = tabulated.
|
[Integer]
|
0
|
|
-E
|
Cost to extend a gap (0 invokes default behavior).
|
[Integer]
|
0
|
|
-F
|
Filter query sequence (DUST with blastn, SEG
with others)
|
[String]
|
T
|
|
-G
|
Cost to open a gap (0 invokes default behavior).
|
[Integer]
|
0
|
|
-I
|
Location on first sequence.
|
[String]
|
|
|
-J
|
Location on second sequence.
|
[String]
|
|
|
-M
|
Matrix.
|
[String]
|
BLOSUM62
|
|
-S
|
Query strands to search against database (blastn
only). 3 is both, 1 is top, 2 is bottom.
|
[Integer]
|
3
|
|
-T
|
Produce HTML output.
|
[T/F]
|
F
|
|
-U
|
Use lowercase filtering for the query sequence.
|
[T/F]
|
F
|
|
-W
|
Wordsize (0 invokes default behavior).
|
[Integer]
|
0
|
|
-X
|
X dropoff value for gapped alignment (in bits) (0 invokes default
behavior).
|
[Integer]
|
0
|
|
-Y
|
Effective length of the search space (use 0 for the real size).
|
[Real]
|
0
|
