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BLAST by Joseph Bedell, Mark Yandell, Ian Korf

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This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
252
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Chapter 13: NCBI-BLAST Reference
-z [real number]
Default: 0
The effective length of a database; same as blastall.
-Z [integer]
Default: 50
The X dropoff value for a dynamic programming gapped extension.
bl2seq Parameters
bl2seq runs the basic BLAST searches on two sequences. Many parameters are identi-
cal 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 connec-
tion 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.)
This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
bl2seq Parameters
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-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 trans-
lating 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.
This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
254
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Chapter 13: NCBI-BLAST Reference
-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.
This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
bl2seq Parameters
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255
-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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