|
-a
|
Number of processors to use.
|
[Integer]
|
1
|
|
-b
|
Number of database sequence to show alignments for (B).
|
[Integer]
|
250
|
|
-d
|
Database: multiple database names are bracketed by quotations, for
example :
-d "db1 db2 db3".
|
[String]
|
nr
|
|
-e
|
Expectation value (E).
|
[Real]
|
10.0
|
|
-f
|
Threshold for extending hits, default if 0.
|
[Integer]
|
0
|
|
-g
|
Perfom gapped alignment (not available with
tblastx).
|
[T/F]
|
T
|
|
-i
|
Query File.
|
[File In]
|
stdin
|
|
-l
|
Restrict search of database to list of GIs.
|
[String]
|
Optional
|
|
-m
|
Alignment view options:
- 0 = Tairwise.
- 1 = Query-anchored, showing identities.
- 2 = Query-anchored, no identities.
- 3 = Flat query-anchored, show identities.
- 4 = Flat query-anchored, no identities.
- 5 = Query-anchored, no identities and blunt ends.
- 6 = Flat query-anchored, no identities and blunt ends.
- 7 = XML Blast output.
- 8 = Tabular.
|
[Integer]
|
0
|
|
-n
|
MegaBLAST search.
|
[T/F]
|
F
|
|
-o
|
BLAST report Output File.
|
[File Out]
|
stdout
|
|
-p
|
Program Name.
|
[String]
|
|
|
-q
|
Penalty for a nucleotide mismatch (blastn only).
|
[Integer]
|
-3
|
|
-r
|
Reward for a nucleotide match (blastn only).
|
[Integer]
|
1
|
|
-v
|
Number of database sequences to show one-line descriptions for (V).
|
[Integer]
|
500
|
|
-y
|
Dropoff (X) for blast extensions in bits (0.0 invokes default
behavior).
|
[Real]
|
0.0
|
|
-z
|
Effective length of the database (use 0 for the real size).
|
[Real]
|
0
|
|
-A
|
Multiple Hits window size (0 for single-hit algorithm).
|
[Integer]
|
40
|
|
-D
|
DB Genetic code (for
tblast[nx] only).
|
[Integer]
|
1
|
|
-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
|
Show GIs in deflines.
|
[T/F]
|
F
|
|
-J
|
Believe the query defline.
|
[T/F]
|
F
|
|
-K
|
Number of best hits from a region to keep (off by default; if used, a
value of 100 is recommended).
|
[Integer]
|
0
|
|
-L
|
Location on query sequence.
|
[String]
|
|
|
-M
|
Matrix.
|
[String]
|
BLOSUM62
|
|
-O
|
SeqAlign file.
|
[File Out]
|
|
|
-P
|
- 0 = Multiple hits, 1-pass.
- 1 = Single hit, 1-pass.
- 2 = 2-pass.
|
[Integer]
|
0
|
|
-Q
|
Query Genetic code to use.
|
[Integer]
|
1
|
|
-R
|
PSI-TBLASTN checkpoint file.
|
[File In]
|
|
|
-S
|
Query strands to search against database (for
blast[nx], and
tblastx). 3 is both, 1 is top, 2 is bottom.
|
[Integer]
|
3
|
|
-T
|
Produce HTML output.
|
[T/F]
|
F
|
|
-U
|
Use lower case filtering of FASTA sequence.
|
[T/F]
|
F
|
|
-W
|
Word size, default if 0.
|
[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
|
|
-Z
|
X dropoff value for final gapped alignment (in bits).
|
[Integer]
|
0
|
