Position-Specific Iterated BLAST
(PSI-BLAST) is an iterative search in which sequences found in one
round of searching are used to build a score model for the next round
of searching. For details, see Section 7.1 at the end of this
chapter.
An example of PSI-BLAST command-line entry:
blastpgp -i queryfilename -B alignmentfilename -j 2 -d databasefilename where -j 2 indicates to search for 2 rounds.
Most BLAST options can be used with PSI-BLAST. However, there are
several blastpgp parameters specifically for
PSI-BLAST. The following table summarizes these PSI-BLAST options.
|
-c
|
"Constant"used in the pseudocount
formula.
|
[Integer]
|
10
|
|
-h
|
e-value threshold for including sequences in the score matrix model.
|
[Real]
|
0.001
|
|
-j
|
Maximum number of rounds.
|
[Integer]
|
1
|
|
-B
|
Provides a way to jump start PSI-BLAST from a master-slave multiple
alignment computed outside PSI-BLAST.
|
[File In]
|
|
|
-C
|
Stores the query and frequency count ratio matrix in a file.
|
[File Out]
|
|
|
-Q
|
Output File for PSI-BLAST Matrix in ASCII.
|
[File Out]
|
|
|
-R
|
Restarts from a file stored previously.
|
[File In]
|
|
|
-T
|
Produce HTML output [T/F].
|
[T/F]
|
F
|
|
