blastall

blastall

blastall allows use of all BLAST programs (blastn, blastp, blastx, tblastx, and tblastn). The following table summarizes the query, database sequence, and alignment types for the various BLAST commands.

Program

Query sequence type

Database sequence type

Alignment sequence type

blastn

nucleotide

nucleotide

nucleotide

blastp

protein

protein

protein

blastx

nucleotide

protein

protein

tblastn

protein

nucleotide

protein

tblastx

nucleotide

nucleotide

protein

An example of a blastall command-line entry:

blastall -p programname -d databasefilename -i queryfilename -o outputfilename

The following table summarizes the blastall 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

-d

Database: multiple database names are bracketed by quotations, for example :

-d "db1 db2 db3".

[String]

nr

-e

Expectation value (E).

[Real]

10.0

-f

Threshold for extending hits, default if 0.

[Integer]

0

-g

Perfom gapped alignment (not available with tblastx).

[T/F]

T

-i

Query File.

[File In]

stdin

-l

Restrict search of database to list of GIs.

[String]

Optional

-m

Alignment view options:

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

[Integer]

0

-n

MegaBLAST search.

[T/F]

F

-o

BLAST report Output File.

[File Out]

stdout

-p

Program Name.

[String]

 

-q

Penalty for a nucleotide mismatch (blastn only).

[Integer]

-3

-r

Reward for a nucleotide match (blastn only).

[Integer]

1

-v

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

[Integer]

500

-y

Dropoff (X) for blast extensions in bits (0.0 invokes default behavior).

[Real]

0.0

-z

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

[Real]

0

-A

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

[Integer]

40

-D

DB Genetic code (for tblast[nx] only).

[Integer]

1

-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

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 (off by default; if used, a value of 100 is recommended).

[Integer]

0

-L

Location on query sequence.

[String]

 

-M

Matrix.

[String]

BLOSUM62

-O

SeqAlign file.

[File Out]

 

-P

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

[Integer]

0

-Q

Query Genetic code to use.

[Integer]

1

-R

PSI-TBLASTN checkpoint file.

[File In]

 

-S

Query strands to search against database (for blast[nx], and tblastx). 3 is both, 1 is top, 2 is bottom.

[Integer]

3

-T

Produce HTML output.

[T/F]

F

-U

Use lower case filtering of FASTA sequence.

[T/F]

F

-W

Word size, default if 0.

[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

-Z

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

[Integer]

0



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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