word_size

Blastx

integer

3

Word size for initial match. Valid word sizes are 2-7.

word_size

Blastx-fast

Integer

6

Word size for initial match.

gapopen

All

integer

11

Cost to open a gap.

gapextend

All

integer

1

Cost to extend a gap.

matrix

All

string

BLOSUM62

Scoring matrix name.

threshold

Blastx

integer

12

Minimum score to add a word to the BLAST lookup table.

threshold

Blastx-fast

Integer

21

Minimum score to add a word to the BLAST lookup table.

seg

All

string

12 2.2 2.5

Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable).

soft_masking

all

boolean

false

Apply filtering locations as soft masks (i.e., only for finding initial matches).

lcase_masking

all

flag

N/A

Use lower case filtering in query and subject sequence(s).

db_soft_mask

all

integer

none

Filtering algorithm ID to apply to the BLAST database as soft mask (i.e., only for finding initial matches).

db_hard_mask

all

integer

none

Filtering algorithm ID to apply to the BLAST database as hard mask (i.e., sequence is masked for all phases of search).

xdrop_gap_final

all

real

25

Heuristic value (in bits) for final gapped alignment.

window_size

all

integer

40

Multiple hits window size, use 0 to specify 1-hit algorithm.

strand

all

string

both

Query strand(s) to search against database/subject. Choice of both, minus, or plus.

query_genetic_code

all

integer

1

Genetic code to translate query, see ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt

max_intron_length

all

integer

0

Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments (a negative value disables linking).

comp_based_stats

all

integer

2

Use composition-based statistics for blastx:

D or d: default (equivalent to 2)

0 or F or f: no composition-based statistics

1: Composition-based statistics as in NAR 29:2994-3005, 2001

2 or T or t : Composition-based score adjustment as in Bioinformatics

21:902-911, 2005, conditioned on sequence properties

3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally

Default = `2'