|
-a
|
Number of processors to use.
|
[Integer]
|
1
|
|
-b
|
Number of database sequence to show alignments for (B).
|
[Integer]
|
250
|
|
-c
|
Constant in pseudocounts for multipass version.
|
[Integer]
|
9
|
|
-d
|
Database.
|
[String]
|
nr
|
|
-e
|
Expectation value (E).
|
[Real]
|
10.0
|
|
-f
|
Threshold for extending hits.
|
[Integer]
|
0
|
|
-g
|
Gapped.
|
[T/F]
|
T
|
|
-h
|
e-value threshold for inclusion in multipass model.
|
[Real]
|
0.005
|
|
-i
|
Query File.
|
[File In]
|
stdin
|
|
-j
|
Maximum number of passes to use in multipass version.
|
[Integer]
|
1
|
|
-k
|
Hit File for PHI-BLAST.
|
[File In]
|
hit_file
|
|
-l
|
Restrict search of database to list of GIs.
|
[String]
|
|
|
-m
|
Alignment view options:
- 0 = Pairwise
- 1 = Query-anchored, showing identities.
- 2 = Query-anchored, no identities.
- 3 = Flat query-anchored, show identities.
- 4 = Flat query-anchored, no identities.
- 5 = qQuery-anchored no identities and blunt ends.
- 6 = Flat query-anchored, no identities and blunt ends.
- 7 = XML Blast output.
- 8 = Tabular output.
|
[Integer]
|
0
|
|
-o
|
Output file for alignment.
|
[File Out]
|
stdout
|
|
-p
|
Program option for PHI-BLAST.
|
[String]
|
blastpgp
|
|
-s
|
Compute locally optimal Smith-Waterman alignments.
|
[T/F]
|
F
|
|
-t
|
Tweak Lambda, K, and score matrix for each match.
|
[T/F]
|
T
|
|
-v
|
Number of database sequences to show one-line descriptions for (V).
|
[Integer]
|
500
|
|
-y
|
Dropoff (X) for blast extensions in bits (default if 0).
|
[Real]
|
7.0
|
|
-z
|
Effective length of the database (use 0 for the real size).
|
[Integer]
|
0
|
|
-A
|
Multiple hits window size (0 for single-hit algorithm).
|
[Integer]
|
40
|
|
-B
|
Input alignment file for PSI-BLAST restart.
|
[File In]
|
|
|
-C
|
Output file for PSI-BLAST checkpointing.
|
[File Out]
|
|
|
-E
|
Cost to extend a gap.
|
[Integer]
|
1
|
|
-F
|
Filter query sequence with SEG.
|
[String]
|
F
|
|
-G
|
Cost to open a gap.
|
[Integer]
|
11
|
|
-H
|
End of required region in query (-1 indicates end of query).
|
[Integer]
|
-1
|
|
-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.
|
[Integer]
|
0
|
|
-L
|
Cost to decline alignment (disabled when 0).
|
[Integer]
|
0
|
|
-M
|
Matrix.
|
[String]
|
BLOSUM62
|
|
-N
|
Number of bits to trigger gapping.
|
[Real]
|
22.0
|
|
-O
|
SeqAlign file ("Believe the query
defline" must be TRUE).
|
[File Out]
|
Optional
|
|
-P
|
- 0 = Multiple hits, 1-pass.
- 1 = Single hit, 1-pass.
- 2 = 2-pass.
|
[Integer]
|
0
|
|
-Q
|
Output file for PSI-BLAST matrix in ASCII.
|
[File Out]
|
|
|
-R
|
Input file for PSI-BLAST restart.
|
[File In]
|
|
|
-S
|
Start of required region in query.
|
[Integer]
|
1
|
|
-T
|
Produce HTML output.
|
[T/F]
|
F
|
|
-U
|
Use lowercase filtering of FASTA sequence.
|
[T/F]
|
F
|
|
-W
|
Word size, default if 0.
|
[Integer]
|
0
|
|
-X
|
X dropoff value for gapped alignment (in bits).
|
[Integer]
|
15
|
|
-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]
|
25
|
