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

PHI-BLAST

PHI-BLAST (Pattern-Hit Initiated BLAST) is a search program that combines matching of regular expressions with local alignments surrounding the match.

An example of a PHI-BLAST command-line entry:

blastpgp -i queryfilename -k patternfilename -p patseedp

where patseedp indicates the mode of usage.

Most BLAST options can be used with PHI-BLAST. However, the use of the -g F option is forbidden because PHI-BLAST requires gapped alignments.

The syntax for patterns in PHI-BLAST follows the conventions of PROSITE. All PROSITE codes are allowed, but only the ID, PA, and HI codes are relevant to PHI-BLAST.

Here is an example of a pattern:

ID  ER_TARGET; PATTERN.
PA  [KRHQSA]-[DENQ]-E-L>.
HI (19 22)
HI (201 204)
bl2seq

bl2seq (BLAST 2 Sequences) allows for the alignment of two given sequences.

An example of a bl2seq command-line entry:

bl2seq -p programname -i firstfilename -j secondfilename -o
  <outputfilenanme>

The following table summarizes the bl2seq options.

Option

Definition

Type

Default

-a

SeqAnnot output file.

[File Out]

 

-d

Theoretical database size (0 is real size).

[Integer]

0

-e

Expectation value (E).

[Real]

10.0

-g

Gapped.

[T/F]

T

-i

First sequence.

[File In]

 

-j

Second sequence.

[File In]

 

-m

Use MegaBLAST for search.

[T/F]

F

-o

Alignment output file.

[File Out]

stdout

-p

Program name: blastp, blastn, blastx, tblastn, tblastx. For blastx, the first sequence should be nucleotide; for tblastn, the 2nd sequence sequence should be nucleotide.

[String]

 

-q

Penalty for a nucleotide mismatch (blastn only).

[Integer]

-3

-r

Reward for a nucleotide match (blastn only).

[Integer]

1

-t

Length of the largest intron allowed in tblastn for linking HSPs.

[Integer]

0

-A

Input sequences in the form of <accession.version>.

[T/F]

F

-D

Output format: 0 = traditional; 1 = tabulated.

[Integer]

0

-E

Cost to extend a gap (0 invokes default behavior).

[Integer]

0

-F

Filter query sequence (DUST with blastn, SEG with others)

[String]

T

-G

Cost to open a gap (0 invokes default behavior).

[Integer]

0

-I

Location on first sequence.

[String]

 

-J

Location on second sequence.

[String]

 

-M

Matrix.

[String]

BLOSUM62

-S

Query strands to search against database (blastn only). 3 is both, 1 is top, 2 is bottom.

[Integer]

3

-T

Produce HTML output.

[T/F]

F

-U

Use lowercase filtering for the query sequence.

[T/F]

F

-W

Wordsize (0 invokes default behavior).

[Integer]

0

-X

X dropoff value for gapped alignment (in bits) (0 invokes default behavior).

[Integer]

0

-Y

Effective length of the search space (use 0 for the real size).

[Real]

0