PSI-BLAST

PSI-BLAST

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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.

Option	Definition	Type	Default
-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