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-reviews2002.10   doi:10.1186/gb-2001-2-10-reviews2002