word_size

integer

3

Word size for initial match.

matrix

string

BLOSUM62

Scoring matrix name.

threshold

integer

13

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

seg

string

12 2.2 2.5

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

soft_masking

boolean

false

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

lcase_masking

flag

N/A

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

db_soft_mask

integer

none

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

db_hard_mask

integer

none

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

strand

string

both

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

query_genetic_code

integer

1

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

db_gen_code

integer

1

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

max_intron_length

integer

0

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