bl2seq

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



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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