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BLAST parameters and options |
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| Parameter |
Use |
Parameter type |
Default setting |
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| (a) Parameters mentioned in the text and Box 2 |
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| -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 |
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| -i |
Name of the query file |
Filename |
"stdin" |
| -m |
Alignment viewing options, which include: |
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| 0 Pairwise alignment |
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| 1 Query-anchored showing identities |
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| 2 Query-anchored, no identities |
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| 7 XML output |
Integer |
0 |
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| -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 |
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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 |
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