General Search Options

• -evalue <Real>
    Expectation value (E) threshold for saving hits
    Default = '10'

• -word_size <Integer, >=2>
    Word size for wordfinder algorithm

• -gapopen <Integer>
    Cost to open a gap
    Default: '11'

• -gapextend <Integer>
    Cost to extend a gap
    Default: '1'

• -matrix <String>
    Scoring matrix name (normally BLOSUM62)
    Default: 'BLOSUM62'

• -threshold <Real, >=0>
    Minimum word score such that the word is added to the BLAST lookup
    table

• -comp_based_stats <String>
    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
        properties
        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
    or 0
    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

• -seg <String>
    Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
    or 'no' to disable)
    BLASTP: Default = 'no'
    BLASTX: Default = 'yes'

• -soft_masking <Boolean>
    Apply filtering locations as soft masks
    Default = 'false'

• -lcase_masking
    Use lower case filtering in query and subject sequence(s)?

Restrict search or results

• -gilist <String>
    Restrict search of database to list of GI's
      * Incompatible with:  negative_gilist, seqidlist, remote, subject,
    subject_loc

• -seqidlist <String>
    Restrict search of database to list of SeqId's
      * Incompatible with:  gilist, negative_gilist, remote, subject,
    subject_loc

• -negative_gilist <String>
    Restrict search of database to everything except the listed GIs
      * Incompatible with:  gilist, seqidlist, remote, subject,
        subject_loc

• -entrez_query <String>
    Restrict search with the given Entrez query
      * Requires:  remote

• -db_soft_mask <String>
    Filtering algorithm ID to apply to the BLAST database as soft masking
      * Incompatible with:  subject, subject_loc

• -culling_limit <Integer, >=0>
    If the query range of a hit is enveloped by that of at least this
    many higher-scoring hits, delete the hit
      * Incompatible with:  best_hit_overhang, best_hit_score_edge

• -best_hit_overhang <Real, (>0 and <0.5)>
    Best Hit algorithm overhang value (recommended value: 0.1)
      * Incompatible with:  culling_limit

• -best_hit_score_edge <Real, (>0 and <0.5)>
    Best Hit algorithm score edge value (recommended value: 0.1)
      * Incompatible with:  culling_limit

• -max_target_seqs <Integer, >=1>
    Maximum number of aligned sequences to keep