July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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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.
This is ...
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.