The complete arguments for BLASTALL 2.2.4
- -p
- Program Name [String]
- -d
- Database [String]
default = nr
-
-i
- Query File [File In]
default = stdin
- -e
- Expectation value (E) [Real]
default = 10.0
- -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]
default = 0
- -o
- BLAST report Output File [File Out] Optional
default = stdout
-
-F
-
Filter query sequence (DUST with blastn, SEG with others) [String]
default = T
- -G
-
Cost to open a gap (zero invokes default behavior) [Integer]
default = 0
- -E
-
Cost to extend a gap (zero invokes default behavior) [Integer]
default = 0
- -X
-
X dropoff value for gapped alignment (in bits) (zero invokes default behavior)
blastn 30, megablast 20, tblastx 0, all others 15 [Integer]
default = 0
- -I
- Show GI's in deflines [T/F]
default = F
- -q
- Penalty for a nucleotide mismatch (blastn only) [Integer]
default = -3
- -r
- Reward for a nucleotide match (blastn only) [Integer]
default = 1
- -v
- Number of database sequences to show one-line descriptions for (V) [Integer]
default = 500
- -b
- Number of database sequence to show alignments for (B) [Integer]
default = 250
- -f
- Threshold for extending hits, default if zero
blastp 11, blastn 0, blastx 12, tblastn 13
tblastx 13, megablast 0 [Integer]
default = 0
- -g
- Perfom gapped alignment (not available with tblastx) [T/F]
default = T
- -Q
- Query Genetic code to use [Integer]
default = 1
- -D
- DB Genetic code (for tblast[nx] only) [Integer]
default = 1
- -a
- Number of processors to use [Integer]
default = 1
- -O
- SeqAlign file [File Out] Optional
- -J
- Believe the query defline [T/F]
default = F
- -M
- Matrix [String]
default = BLOSUM62
- -W
- Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer]
default = 0
- -z
- Effective length of the database (use zero for the real size) [Real]
default = 0
- -K
- Number of best hits from a region to keep (off by default, if used a value of 100 is recommended) [Integer]
default = 0
- -Y
- Effective length of the search space (use zero for the real size) [Real]
default = 0
- -S
- Query strands to search against database (for blast[nx], and tblastx)
3 is both, 1 is top, 2 is bottom [Integer]
default = 3
- -T
- Produce HTML output [T/F]
default = F
- -l
- Restrict search of database to list of GI's [String] Optional
- -U
- Use lower case filtering of FASTA sequence [T/F] Optional
default = F
- -y
- X dropoff value for ungapped extensions in bits (0.0 invokes default behavior)
blastn 20, megablast 10, all others 7 [Real]
default = 0.0
- -Z
- X dropoff value for final gapped alignment in bits (0.0 invokes default behavior)
blastn/megablast 50, tblastx 0, all others 25 [Integer]
default = 0
- -R
- PSI-TBLASTN checkpoint file [File In] Optional
- -n
- MegaBlast search [T/F]
default = F
- -L
- Location on query sequence [String] Optional
- -A
- Multiple Hits window size, default if zero (blastn/megablast 0, all others 40 [Integer]
default = 0
- -w
- Frame shift penalty (OOF algorithm for blastx) [Integer]
default = 0
- -t
- Length of the largest intron allowed in tblastn for linking HSPs (0 disables linking) [Integer]
default = 0