-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 = query-anchored no identities and blunt ends,
6 = flat query-anchored, no identities and blunt ends,
7 = XML Blast output,
8 = tabular,
9 tabular with comment lines
[Integer]
|
-e
|
Expectation value (E)
|
-F
|
Filter query sequence (DUST with blastn, SEG with others) [T/F]
|
-G
|
Cost to open a gap (zero invokes default behavior)
|
-E
|
Cost to extend a gap (zero invokes default behavior)
|
-X
|
X dropoff value for gapped alignment (in bits) (zero invokes default behavior)
blastn 30, megablast 20, tblastx 0, all others 15
|
-I
|
Show GI's in deflines [T/F]
|
-q
related: p
|
Penalty for a nucleotide mismatch (blastn only)
|
-r
related: p
|
Reward for a nucleotide match (blastn only)
|
-v
|
Number of database sequences to show one-line descriptions for (V)
|
-b
|
Number of database sequence to show alignments for (B)
|
-f
|
Threshold for extending hits, default if zero
blastp 11, blastn 0, blastx 12, tblastn 13
tblastx 13, megablast 0
|
-g
conflicted: p |
Perfom gapped alignment (not available with tblastx)
|
-Q
|
Query Genetic code to use
|
-D
related: p
|
DB Genetic code (for tblast[nx] only)
|
-a
|
Number of processors to use
|
-J
|
Believe the query defline [T/F]
|
-M
|
Matrix
|
-W
|
Word size, default if zero (blastn 11, megablast 28, all others 3)
|
-z
|
Effective length of the database (use zero for the real size) [Real]
|
-K
|
Number of best hits from a region to keep (off by default, if used a value of 100 is recommended)
|
-P
|
0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer]
|
-Y
|
Effective length of the search space (use zero for the real size) [Real]
|
-S
related: p
|
Query strands to search against database (for blastx, and tblastx)
3 is both, 1 is top, 2 is bottom
|
-T
|
Produce HTML output [T/F]
|
-l
|
Restrict search of database to list of GI's [String] Optional
true
false |
-U
|
Use lower case filtering of FASTA sequence [T/F] Optional
|
-y
|
X dropoff value for ungapped extensions in bits (0.0 invokes default behavior)
blastn 20, megablast 10, all others 7 [Real]
|
-Z
|
X dropoff value for final gapped alignment in bits (0.0 invokes default behavior)
blastn/megablast 50, tblastx 0, all others 25
|
-n
|
MegaBlast search [T/F]
|
-L
|
Location on query sequence
|
-A
|
Multiple Hits window size, default if zero (blastn/megablast 0, all others 40
|
-w
|
Frame shift penalty (OOF algorithm for blastx)
|
-t
related: p
|
Length of the largest intron allowed in tblastn for linking HSPs (0 disables linking)
|
-B
|
Number of concatenated queries, for blastn and tblastn [Integer] Optional
|
-V
|
Force use of old engine [T/F] Optional
|
-C
|
Use composition-based statistics for tblastn:
D or d: default (equivalent to F)
0 or F or f: no composition-based statistics
1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001
2: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally
For programs other than tblastn, must either be absent or be D, F or 0 [String]
|
-s
|
Compute locally optimal Smith-Waterman alignments (This option is only available for gapped tblastn.) [T/F]
|
