Table 3.

BLAST parameters and options

Parameter	Use	Parameter type	Default setting
(a) Parameters mentioned in the text and Box 2
-M	Matrix	String	BLOSUM62
-r	Reward for a nucleotide match (BLASTNonly)	Integer	1
-q	Penalty for a nucleotide mismatch (BLASTNonly)	Integer	-3
-G	Cost to open a gap (zero invokes default behavior)	Integer	0
-E	Cost to extend a gap (zero invokes default behavior)	Integer	0
-F	Filter query sequence	String	T
-W	Word size; default length is used if set to zero	Integer	0
-z	Effective length of the database (use zero to get the real size)	Real	0
-e	Expectation value (E)	Real	10.0
(b) Additional useful parameters
-i	Name of the query file	Filename	"stdin"
-m	Alignment viewing options, which include:
	0 Pairwise alignment
	1 Query-anchored showing identities
	2 Query-anchored, no identities
	7 XML output	Integer	0
-o	Name of the BLAST report output file	Filename	"stdout"
-f	Threshold for extending hits; default is used if set to zero	Integer	0
-g	Perform gapped alignment (not available with TBLASTX)	T/F	T
-Y	Effective length of the search space (use zero get the real size)	Real	0
-S	Query strands to search against the database (for BLAST [NX], and TBLASTX) 3 is both, 1 is top, 2 is bottom	Integer	3
-T	Produce HTML output	T/F	F
-y	Drop-off (X) for BLAST extensions, in bits (0.0 invokes default behavior)	Real	0.0
-Z	X drop-off value for final gapped alignment (in bits)	Integer	0

Parameters are preceded by a dash when used with the stand-alone version of BLAST; the web interfaces uses boxes and drop-down menus to control many of the same parameters. Parameters are given in the table in the order that they are mentioned in the text or on using NCBI-BLAST; additional parameters are listed at the NCBI [38]. Abbreviations: T/F, true or false; for BLAST variants see Table 1. 'Query-anchored' means that the query string is used as the 'top line' of the alignment.