PSI-BLAST

PSI-BLAST

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



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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