blast/docs/full_options.html
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<title>NCBI BLAST Advanced Options</title>
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<h1>Full list of the BLAST Advanced options</h1>
<UL>
<LI> <a href = "#blastn">blastn</a>
<LI> <a href = "#blastp">blastp</a>
<LI> <a href = "#blastx">blastx</a>
<LI> <a href = "#tblastn">tblastn</a>
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<h3><a name = blastn><FONT color="green">
BLASTN Program Advanced Options</FONT></a></h3>
<PRE>
-G Cost to open a gap [Integer]
default = 5
-E Cost to extend a gap [Integer]
default = 2
-q Penalty for a mismatch in the blast portion of run [Integer]
default = -3
-r Reward for a match in the blast portion of run [Integer]
default = 1
-e Expectation value (E) [Real]
default = 10.0
-W Word size, default is 11 for blastn, 3 for other programs.
-v Number of one-line descriptions (V) [Integer]
default = 100
-b Number of alignments to show (B) [Integer]
default = 100
</PRE>
<HR>
<h3><a name = blastp><FONT color="green">
BLASTP Program Advanced Options</FONT></a></h3>
<h3><a name = blastx><FONT color="green">
BLASTX Program Advanced Options</FONT></a></h3>
<h3><a name = tblastn><FONT color="green">
TBLASTN Program Advanced Options</FONT></a></h3>
<PRE>
-G Cost to open a gap [Integer]
default = 11
-E Cost to extend a gap [Integer]
default = 1
-e Expectation value (E) [Real]
default = 10.0
-W Word size, default is 11 for blastn, 3 for other programs.
-v Number of one-line descriptions (V) [Integer]
default = 100
-b Number of alignments to show (B) [Integer]
default = 100
Limited values for gap existence and extension are supported for these three programs.
Some supported and suggested values are:
Existence Extension
10 1
10 2
11 1
8 2
9 2
</PRE>
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<!-- Created: Mon Jun 16 12:38:19 EDT 1997 -->
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Last modified: Mon July 31, 1997
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