blastpgp

blastpgp

blastpgp performs gapped blastp searches and can be used to perform iterative searches in psi-blast and phi-blast mode.

An example of a blastpgp command-line entry:

blastpgp -i queryfilename -B alignmentfilename -j 2 -d databasefilename

The following table summarizes the blastpgp options.

Option

Definition

Type

Default

-a

Number of processors to use.

[Integer]

1

-b

Number of database sequence to show alignments for (B).

[Integer]

250

-c

Constant in pseudocounts for multipass version.

[Integer]

9

-d

Database.

[String]

nr

-e

Expectation value (E).

[Real]

10.0

-f

Threshold for extending hits.

[Integer]

0

-g

Gapped.

[T/F]

T

-h

e-value threshold for inclusion in multipass model.

[Real]

0.005

-i

Query File.

[File In]

stdin

-j

Maximum number of passes to use in multipass version.

[Integer]

1

-k

Hit File for PHI-BLAST.

[File In]

hit_file

-l

Restrict search of database to list of GIs.

[String]

 

-m

Alignment view options:

0 = Pairwise
1 = Query-anchored, showing identities.
2 = Query-anchored, no identities.
3 = Flat query-anchored, show identities.
4 = Flat query-anchored, no identities.
5 = qQuery-anchored no identities and blunt ends.
6 = Flat query-anchored, no identities and blunt ends.
7 = XML Blast output.
8 = Tabular output.

[Integer]

0

-o

Output file for alignment.

[File Out]

stdout

-p

Program option for PHI-BLAST.

[String]

blastpgp

-s

Compute locally optimal Smith-Waterman alignments.

[T/F]

F

-t

Tweak Lambda, K, and score matrix for each match.

[T/F]

T

-v

Number of database sequences to show one-line descriptions for (V).

[Integer]

500

-y

Dropoff (X) for blast extensions in bits (default if 0).

[Real]

7.0

-z

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

[Integer]

0

-A

Multiple hits window size (0 for single-hit algorithm).

[Integer]

40

-B

Input alignment file for PSI-BLAST restart.

[File In]

 

-C

Output file for PSI-BLAST checkpointing.

[File Out]

 

-E

Cost to extend a gap.

[Integer]

1

-F

Filter query sequence with SEG.

[String]

F

-G

Cost to open a gap.

[Integer]

11

-H

End of required region in query (-1 indicates end of query).

[Integer]

-1

-I

Show GIs in deflines.

[T/F]

F

-J

Believe the query defline.

[T/F]

F

-K

Number of best hits from a region to keep.

[Integer]

0

-L

Cost to decline alignment (disabled when 0).

[Integer]

0

-M

Matrix.

[String]

BLOSUM62

-N

Number of bits to trigger gapping.

[Real]

22.0

-O

SeqAlign file ("Believe the query defline" must be TRUE).

[File Out]

Optional

-P

0 = Multiple hits, 1-pass.
1 = Single hit, 1-pass.
2 = 2-pass.

[Integer]

0

-Q

Output file for PSI-BLAST matrix in ASCII.

[File Out]

 

-R

Input file for PSI-BLAST restart.

[File In]

 

-S

Start of required region in query.

[Integer]

1

-T

Produce HTML output.

[T/F]

F

-U

Use lowercase filtering of FASTA sequence.

[T/F]

F

-W

Word size, default if 0.

[Integer]

0

-X

X dropoff value for gapped alignment (in bits).

[Integer]

15

-Y

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

[Real]

0

-Z

X dropoff value for final gapped alignment (in bits).

[Integer]

25



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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