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.

Pertsemlidis and Fondon Genome Biology 2001 2:reviews2002.1   doi:10.1186/gb-2001-2-10-reviews2002