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Chapter 13: NCBI-BLAST Reference
-p [real number]
Default: 0
Percent identity cutoff. Alignments less than [real number] aren’t reported. If using -D 0, all
alignments are kept regardless of percent identity (no trace-back is performed, so percent
identity can’t be calculated).
-P [integer]
Default: 0
The maximum number of positions for a hash value. If set to nonzero, redundant subse-
quences will be masked in the word seeding phase. This allows a simple type of filtering by
masking out subsequences that occur in the query sequences more than
[integer] times.
When the word size (
-W) is set to 16 or higher, -P applies to subsequences of length 12; it
applies to subsequences of length 8 when -
W is set less than 16.
-q [negative integer]
Default: -3
Mismatch penalty; same as blastall.
-Q [file]
Default: Optional
Masked query output. Each query sequence is reported to [file], but with any region hit
turned to Ns. This works only in conjunction with -
D 2.
-r [integer]
Default: 1
Match score; same as blastall.
-R [T/F]
Default: Optional
Reports a short log message at the end of the run.
-s [integer]
Default: Optional
The minimum hit score to report. All alignments scoring less than [integer] aren’t
reported. By default, this is set to the word size, which results in all hits being reported.
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megablast Parameters
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-S [0..3]
Default: 3
The strands to search; same as blastall.
-t [16,18,21]
Default: Optional
Sets discontiguous template size. This, combined with the word size (-W) of either 11 or 12
and the template type (
-N), sets discontiguous megablast.
-T [T/F]
Default: F
The HTML output; same as blastall, but is active only if -D 2 is set.
-U [T/F]
Default: F
Lowercase filtering; same as blastall.
-v [integer]
Default: 500
The number of one-line descriptions. Same as blastall if -D 2 is set.
-W [integer]
Default: 28
Word size. The default word size is very high because sequences aligned by megablast are
expected to be nearly identical. For discontiguous searches (
-t), word size can be only 11
or 12. megablast generates words every four bases (similar to the WU-BLAST
wink param-
eter), so using a word size divisible by four assures that all words of that size will be found.
-X [integer]
Default: 20
The X dropoff value for a gapped alignment; same as blastall.
-y [integer]
Default: 10
The X dropoff value for an ungapped extension; same as blastall.
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