Expectation value (E) threshold for saving hits
Default = '10'
-word_size <Integer, >=2>
Word size for wordfinder algorithm
Cost to open a gap
Cost to extend a gap
Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup
Use composition-based statistics for blastp / tblastn:
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
3: Composition-based score adjustment as in Bioinformatics
21:902-911, 2005, unconditionally
For programs other than tblastn, must either be absent or be D, F
Default = `2'
-num_descriptions <Integer, >=0>
Number of database sequences to show one-line descriptions for
Default = `500'
-num_alignments <Integer, >=0>
Number of database sequences to show alignments for
Default = `250'
Query filtering options
Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
or 'no' to disable)
Default = `no'