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blastpgp Parameters (PSI-BLAST and PHI-BLAST)
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-j [integer]
Default: 1
The maximum number of passes to use in a multipass version. The default of 1 is just a
regular BLASTP search.
-J [T/F]
Default: F
Believes the query definition line; same as blastall.
-k [file]
Default: hit_file
Program: PHI-BLAST only
Specifies the file containing the PROSITE pattern to be used for seeding in a PHI-BLAST
run. If -
k isn’t specified when running PHI-BLAST (e.g. -p patseedp or -p seedp), the
program looks for a file called hit_file
.
-K [integer]
Default: 0 - Off
The number of best hits from a region to keep; same as blastall.
-l [string]
Default: Optional
Restricts the search of the database to a list of GIs; same as blastall.
-L [integer]
Default: 0 (disabled)
The cost to decline an alignment.
-m [0..9]
Default: 0
Alignment view options; same as blastall.
-M [string]
Default: BLOSUM62
The matrix; same as blastall.
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262
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Chapter 13: NCBI-BLAST Reference
-N [real number]
Default: 22.0
The number of bits required to trigger gapping.
-o [file]
Default: Optional
The output file for alignment; same as blastall.
-O [file]
Default: Optional
A SeqAlign file output; same as blastall.
-p [string]
Default: blastpgp
Specifies whether to run in PSI- or PHI-BLAST mode.
Options
blastpgp
PSI-BLAST mode
patseedp
PHI-BLAST mode. Uses all occurrences of the hit_file pattern to seed alignments. Any
HI tags (see later) in the hit_file are ignored.
seedp
PHI-BLAST mode. The specified pattern is found more than once in the query, and the
hit_file specifies which to use as seeds. The specific pattern(s) occurrences to use is
specified with the
HI tag in the hit_file. For example, the following hit_file designates
seeding from a pattern that occurs at position 143 of the coelacanth HoxA11 protein:
ID HoxA11 pattern2
PA Y-S-[SA]-X-[LVIMK]
HI 143
seedp throws an exception if the hit_file doesn’t contain the HI tags.
-Q [file]
Default: Optional
Output file for a PSI-BLAST matrix in ASCII format. This [file] can’t be used in any
subsequent programs. Use
-c to output a matrix for subsequent searches.
This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
blastpgp Parameters (PSI-BLAST and PHI-BLAST)
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263
-R [file]
Default: Optional
Input checkpoint file for PSI-BLAST restart. Uses the checkpoint file. Output with -c.
-s [T/F]
Default: F
Calculates locally optimal Smith-Waterman alignments. Because of the heuristic nature of
BLAST, it sometimes produces nonoptimal local alignments. This option causes BLAST to
run the full Smith-Waterman alignment algorithm on subjects found by the normal BLAST
heuristic. There may be some speed cost using this option, but it helps guarantee high-
quality alignments, which are important in PSSM generation. Setting -
sTis highly
recommended.
-S [integer]
Default: 1
The start of the required region in query. Used in combination with -H, this sets a specific
region of the query to be used when generating the PSSM.
-t [T/F]
Default: T
Uses composition-based statistics. With this set to T, the score is adjusted based on compo-
sition biases in the query and subject sequences. Using it helps avoid possible corruption of
the PSSM because it introduces low-entropy false positives in the multiple sequence
alignment.
-T [T/F]
Default: F
Produces HTML output; same as blastall.
-U [T/F]
Default: F
Uses lowercase filtering of a query sequence; same as blastall.
-v [integer]
Default: 500
The number of one-line descriptions to show; same as blastall.
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