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General Search Options

<%= ERB::Util.h %q|-evalue 
  Expectation value (E) threshold for saving hits
  Default = '10'| %>

<%= ERB::Util.h %q|-word_size =2>
  Word size for wordfinder algorithm| %>

<%= ERB::Util.h %q|-gapopen 
  Cost to open a gap| %>

<%= ERB::Util.h %q|-gapextend 
  Cost to extend a gap| %>

<%= ERB::Util.h %q|-matrix 
  Scoring matrix name (normally BLOSUM62)| %>

<%= ERB::Util.h %q|-threshold =0>
  Minimum word score such that the word is added to the BLAST lookup
  table| %>

<%= ERB::Util.h %q|-comp_based_stats 
  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'| %>

<%= ERB::Util.h %q|-num_descriptions =0>
  Number of database sequences to show one-line descriptions for
  Default = `500'| %>

<%= ERB::Util.h %q| -num_alignments =0>
  Number of database sequences to show alignments for
  Default = `250'| %>

Query filtering options

<%= ERB::Util.h %q|-seg 
  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
  or 'no' to disable)
  Default = `no'| %>

<%= ERB::Util.h %q|-soft_masking 
  Apply filtering locations as soft masks
  Default = `false'| %>

<%= ERB::Util.h %q|-lcase_masking
  Use lower case filtering in query and subject sequence(s)?| %>

Restrict search or results

<%= ERB::Util.h %q|-gilist 
  Restrict search of database to list of GI's
    * Incompatible with:  negative_gilist, seqidlist, remote, subject,
  subject_loc| %>

<%= ERB::Util.h %q|-seqidlist 
  Restrict search of database to list of SeqId's
    * Incompatible with:  gilist, negative_gilist, remote, subject,
  subject_loc| %>

<%= ERB::Util.h %q|-negative_gilist 
  Restrict search of database to everything except the listed GIs
    * Incompatible with:  gilist, seqidlist, remote, subject,
      subject_loc| %>

<%= ERB::Util.h %q|-entrez_query 
  Restrict search with the given Entrez query
    * Requires:  remote| %>

<%= ERB::Util.h %q|-db_soft_mask 
  Filtering algorithm ID to apply to the BLAST database as soft masking
    * Incompatible with:  subject, subject_loc| %>

<%= ERB::Util.h %q|-culling_limit =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| %>

<%= ERB::Util.h %q|-best_hit_overhang 0 and <0.5)>
  Best Hit algorithm overhang value (recommended value: 0.1)
    * Incompatible with:  culling_limit| %>

<%= ERB::Util.h %q|-best_hit_score_edge 0 and <0.5)>
  Best Hit algorithm score edge value (recommended value: 0.1)
    * Incompatible with:  culling_limit| %>

<%= ERB::Util.h %q|-max_target_seqs =1>
  Maximum number of aligned sequences to keep| %>