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13.7 bl2seq Parameters

bl2seq runs the basic BLAST searches on two sequences. Many parameters are identical between bl2seq and blastall, but some are unique to one program or the other, and some parameters with the same symbol do different things.

Here are a few sample command lines:

bl2seq -p blastp -i protein1 -j protein2
bl2seq -p blastn -i nucleotide1 -j nucleotide2 -F F -D 1
bl2seq -p blastx -i nucleotide -j protein
bl2seq -p tblastn -i protein -j nucleotide
bl2seq -p tblastx -i nucleotide1 -j nucleotide2

The following reference describes the parameters for bl2seq.

-a [file]
Default: Optional

Specifies the SeqAnnot output file. The [file] will be in the Abstract Syntax Notation 1 (ASN.1) format for import into and use with the NCBI toolbox.

-A [T/F]
Default: F

Input sequences are NCBI identifiers. When set to T, the program makes an online connection to the NCBI databases to retrieve the FASTA sequences. 

bl2seq -A -p blastx -i AF287139 -j AAG39070

(This function was just enabled in the 2.2.6 release.)

-d [real number]
Default: 0

Sets the theoretical size of the database. This is useful for maintaining consistent E-values between blastall and bl2seq searches. Identical to the blastall -z parameter. If -d isn't set, the database size is set to the length of the -j sequence.

-D [0/1]
Default: 0

Sets the output format to tabular, which corresponds to the blastall setting -m 8. The other -m report options available in blastall aren't available in bl2seq.

Unlike the blastall parameter of the same name, -D doesn't set the genetic code for translating database sequences. All bl2seq translations use the standard nuclear genetic code.

Options

0

Traditional

1

Tabular

-e [real number]
Default: 10

The expectation value; same as blastall.

-E [integer]
Default: 1

The gap extension value; same as blastall.

-F [T/F] [string]
Default: T

Complexity filtering; same as blastall.

-g [T/F]
Default: T

The gapped alignment; same as blastall.

-G [integer]
Defaults: blastn 5, others 11

The gap initiation penalty; same as blastall.

-i [file]
Default: Required

Sets the input (query) file for the search. For blastx, [file] must be nucleotide, and for tblastn, [file] must be protein. Setting [file] to stdin or using multisequence files isn't recommended.

-I [integer],[integer]
Default: 0,0

The location on the input sequence defined by -i. Follows the blastall -L syntax.

-j [file]
Default: Required

Sets the database file for the search. For blastx, [file] must be protein, and for tblastn, [file] must be nucleotide. Setting [file] to stdin or using multisequence files isn't recommended.

-J [integer],[integer]
Default: 0,0

The location on a sequence defined by -j. Follows the blastall -L syntax.

-m [T/F]
Default: F

Sets a blastn search to megablast mode; same as blastall -n.

-M [string]
Default: BLOSUM62

The scoring matrix, same as blastall.

-o [file]
Default: Optional

The output file; same as blastall.

-p [string]
Default: None, required parameter

The program name; same as blastall.

-q [negative integer]
Default: -3

The nucleotide mismatch score; same as blastall.

-r [integer]
Default: 1

The nucleotide match score; same as blastall.

-S [1..3]
Default: 3

The search strand; same as blastall.

-t [integer]
Default: 0

The longest intron allowed in tblastn for linking HSPs; same as blastall.

-T [T/F]
Default: F

HTML output; same as blastall.

-U [T/F]
Default: F

Lowercase masking; same as blastall.

-W [integer]
Defaults: blastn 11, others 3

The word size; same as blastall.

-X [integer]
Default: blastn 30, others 15

The extension cutoff; same as blastall.

-Y [real number]
Default: 0

The search space; same as blastall.

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