Advance options
| -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 = query-anchored, no identities and blunt ends,
7 = XML Blast output,
8 = tabular,
9 tabular with comment lines [Integer]
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| -e |
Expectation value (E)
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| -F |
Filter query sequence (DUST with blastn, SEG with others) [T/F]
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| -G |
Cost to open a gap (zero invokes default behavior)
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| -E |
Cost to extend a gap (zero invokes default behavior)
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| -X |
X dropoff value for gapped alignment (in bits) (zero invokes default behavior, blastn 30)
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| -I |
Show GI's in deflines [T/F]
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-q
related: p
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Penalty for a nucleotide mismatch (blastn only)
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-r
related: p
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Reward for a nucleotide match (blastn only)
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| -v |
Number of database sequences to show one-line descriptions for (V)
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| -b |
Number of database sequence to show alignments for (B)
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| -f |
Threshold for extending hits, default if zero: blastn 0
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-g
conflicted: p
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Perfom gapped alignment
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| -Q |
Query Genetic code to use
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-D
related: p
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DB Genetic code
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| -a |
Number of processors to use
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| -J |
Believe the query defline [T/F]
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| -M |
Matrix
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| -W |
Word size, default if zero (blastn 11)
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| -z |
Effective length of the database (use zero for the real size) [Real]
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| -K |
Number of best hits from a region to keep (off by default, if used a value of 100 is recommended)
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| -Y |
Effective length of the search space (use zero for the real size) [Real]
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| -T |
Produce HTML output [T/F]
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| -l |
Restrict search of database to list of GI's [String] Optional
true
false
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| -U |
Use lower case filtering of FASTA sequence [T/F] Optional
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| -y |
X dropoff value for ungapped extensions in bits (0.0 invokes default behavior: blastn 20)
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| -Z |
X dropoff value for final gapped alignment in bits (0.0 invokes default behavior)
blastn 50
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| -L |
Location on query sequence
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| -A |
Multiple Hits window size, default if zero (blastn/megablast 0, all others 40
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| -w |
Frame shift penalty (OOF algorithm for blastx)
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-t
related: p
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Length of the largest intron allowed in tblastn for linking HSPs (0 disables linking)
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| -B |
Number of concatenated queries, for blastn and tblastn [Integer] Optional
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| -V |
Force use of old engine [T/F] Optional
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| -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]
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| -s |
Compute locally optimal Smith-Waterman alignments (This option is only available for gapped tblastn.) [T/F]
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