<%# without a space after erb's closing tag, a / gets appended to css' path %>

Blast methods

Nucleotide databases
    <% settings.databases['nucleotide'].each_with_index do |db, i| %>
    • <% end %>

Protein databases
    <% settings.databases['protein'].each_with_index do |db, i| %>
    • <% end %> 
  <%= ERB::Util.h %q|
  -evalue 
    Expectation value (E) threshold for saving hits
    Default = `10'
  -word_size =2>
    Word size for wordfinder algorithm
  -gapopen 
    Cost to open a gap
  -gapextend 
    Cost to extend a gap
  -matrix 
    Scoring matrix name (normally BLOSUM62)
  -threshold =0>
    Minimum word score such that the word is added to the BLAST lookup table
  -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'
  -num_descriptions =0>
    Number of database sequences to show one-line descriptions for
    Default = `500'
  -num_alignments =0>
    Number of database sequences to show alignments for
    Default = `250'
  *** Query filtering options
  -seg 
    Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
    'no' to disable)
    Default = `no'
  -soft_masking 
    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 
    Restrict search of database to list of GI's
      * Incompatible with:  negative_gilist, seqidlist, remote, subject,
    subject_loc
  -seqidlist 
    Restrict search of database to list of SeqId's
      * Incompatible with:  gilist, negative_gilist, remote, subject,
    subject_loc
  -negative_gilist 
    Restrict search of database to everything except the listed GIs
      * Incompatible with:  gilist, seqidlist, remote, subject, subject_loc
  -entrez_query 
    Restrict search with the given Entrez query
      * Requires:  remote
  -db_soft_mask 
    Filtering algorithm ID to apply to the BLAST database as soft masking
      * Incompatible with:  subject, subject_loc
  -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
  -best_hit_overhang 0 and <0.5)>
    Best Hit algorithm overhang value (recommended value: 0.1)
      * Incompatible with:  culling_limit
  -best_hit_score_edge 0 and <0.5)>
    Best Hit algorithm score edge value (recommended value: 0.1)
      * Incompatible with:  culling_limit
  -max_target_seqs =1>
    Maximum number of aligned sequences to keep | %>
<%= @blast %>