sequenceserver 3.0.1 → 3.1.2

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Files changed (64) hide show
  1. checksums.yaml +4 -4
  2. data/bin/sequenceserver +2 -2
  3. data/lib/sequenceserver/api_errors.rb +56 -2
  4. data/lib/sequenceserver/blast/job.rb +20 -3
  5. data/lib/sequenceserver/blast/report.rb +74 -86
  6. data/lib/sequenceserver/blast/tasks.rb +38 -0
  7. data/lib/sequenceserver/blast.rb +6 -0
  8. data/lib/sequenceserver/config.rb +54 -20
  9. data/lib/sequenceserver/database.rb +13 -0
  10. data/lib/sequenceserver/makeblastdb.rb +16 -2
  11. data/lib/sequenceserver/report.rb +0 -6
  12. data/lib/sequenceserver/routes.rb +66 -25
  13. data/lib/sequenceserver/sequence.rb +34 -7
  14. data/lib/sequenceserver/server.rb +1 -1
  15. data/lib/sequenceserver/version.rb +1 -1
  16. data/lib/sequenceserver.rb +1 -1
  17. data/public/404.html +1 -1
  18. data/public/css/app.css +121 -0
  19. data/public/css/app.min.css +1 -0
  20. data/public/css/sequenceserver.css +0 -148
  21. data/public/css/sequenceserver.min.css +3 -3
  22. data/public/js/circos.js +2 -2
  23. data/public/js/collapse_preferences.js +37 -0
  24. data/public/js/databases.js +65 -37
  25. data/public/js/databases_tree.js +2 -1
  26. data/public/js/dnd.js +37 -50
  27. data/public/js/download_fasta.js +1 -0
  28. data/public/js/form.js +79 -50
  29. data/public/js/grapher.js +23 -37
  30. data/public/js/hits_overview.js +2 -2
  31. data/public/js/kablammo.js +2 -2
  32. data/public/js/length_distribution.js +3 -3
  33. data/public/js/null_plugins/grapher/histogram.js +25 -0
  34. data/public/js/null_plugins/options.js +3 -0
  35. data/public/js/null_plugins/query_stats.js +11 -0
  36. data/public/js/null_plugins/report_plugins.js +6 -1
  37. data/public/js/null_plugins/search_header_plugin.js +4 -0
  38. data/public/js/options.js +161 -56
  39. data/public/js/query.js +85 -59
  40. data/public/js/report.js +1 -1
  41. data/public/js/search.js +2 -0
  42. data/public/js/search_button.js +67 -56
  43. data/public/js/sidebar.js +10 -1
  44. data/public/js/tests/database.spec.js +5 -5
  45. data/public/js/tests/form.spec.js +98 -0
  46. data/public/js/tests/mock_data/databases.json +5 -5
  47. data/public/js/tests/mocks/circos.js +6 -0
  48. data/public/js/tests/report.spec.js +4 -3
  49. data/public/js/tests/search_query.spec.js +16 -6
  50. data/public/sequenceserver-report.min.js +46 -24
  51. data/public/sequenceserver-search.min.js +57 -13
  52. data/public/sequenceserver_logo.webp +0 -0
  53. data/views/blastn_options.erb +66 -66
  54. data/views/blastp_options.erb +59 -59
  55. data/views/blastx_options.erb +68 -68
  56. data/views/layout.erb +61 -3
  57. data/views/search.erb +33 -38
  58. data/views/search_layout.erb +153 -0
  59. data/views/tblastn_options.erb +57 -57
  60. data/views/tblastx_options.erb +64 -64
  61. metadata +51 -22
  62. data/lib/sequenceserver/makeblastdb-modified-with-cache.rb +0 -345
  63. data/public/SequenceServer_logo.png +0 -0
  64. data/public/js/tests/advanced_parameters.spec.js +0 -36
data/views/blastp_options.erb CHANGED
@@ -4,40 +4,40 @@
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  characters per line to preserve formatting.
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  %>
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- <h5>General Search Options</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">General Search Options</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short'>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short'>
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  Task to execute
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  Default = 'blastp'|%></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-evalue <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-evalue <Real>
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  Expectation value (E) threshold for saving hits
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  Default = '10'| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-word_size <Integer, >=2>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-word_size <Integer, >=2>
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  Word size for wordfinder algorithm| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-gapopen <Integer>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-gapopen <Integer>
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  Cost to open a gap| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-gapextend <Integer>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-gapextend <Integer>
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  Cost to extend a gap| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-matrix <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-matrix <String>
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  Scoring matrix name (normally BLOSUM62)| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-threshold <Real, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-threshold <Real, >=0>
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  Minimum word score such that the word is added to the BLAST lookup table| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-comp_based_stats <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-comp_based_stats <String>
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  Use composition-based statistics:
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  D or d: default (equivalent to 2)
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  0 or F or f: no composition-based statistics
@@ -52,23 +52,23 @@
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  </ul>
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  <br />
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- <h5>Formatting Options</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">Formatting Options</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-num_descriptions <Integer, >=0>
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  Number of database sequences to show one-line descriptions for
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  Not applicable for outfmt > 4
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  Default = '500'
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  * Incompatible with: max_target_seqs| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -num_alignments <Integer, >=0>
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  Number of database sequences to show alignments for
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  Default = '250'
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  * Incompatible with: max_target_seqs| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q| -sorthits <Integer, (>=0 and =<4)>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -sorthits <Integer, (>=0 and =<4)>
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  Sorting option for hits:
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  alignment view options:
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  0 = Sort by evalue,
@@ -79,7 +79,7 @@
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  Not applicable for outfmt > 4| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q| -sorthsps <Integer, (>=0 and =<4)>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -sorthsps <Integer, (>=0 and =<4)>
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  Sorting option for hps:
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  0 = Sort by hsp evalue,
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  1 = Sort by hsp score,
@@ -92,52 +92,52 @@
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  <br/>
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- <h5>Query filtering options</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">Query filtering options</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-seg <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-seg <String>
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  Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
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  or 'no' to disable)
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  Default = 'no'| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-soft_masking <Boolean>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-soft_masking <Boolean>
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  Apply filtering locations as soft masks
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  Default = 'false'| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-lcase_masking
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-lcase_masking
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  Use lower case filtering in query and subject sequence(s)?| %></pre>
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  </li>
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  </ul>
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  <br/>
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- <h5>Restrict search or results</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">Restrict search or results</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-gilist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-gilist <String>
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  Restrict search of database to list of GIs
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  * Incompatible with: seqidlist, taxids, taxidlist, negative_gilist,
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
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  subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-seqidlist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-seqidlist <String>
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  Restrict search of database to list of SeqIDs
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  * Incompatible with: gilist, taxids, taxidlist, negative_gilist,
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
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  subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-negative_gilist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_gilist <String>
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  Restrict search of database to everything except the specified GIs
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  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
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  subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-negative_seqidlist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_seqidlist <String>
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  Restrict search of database to everything except the specified SeqIDs
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  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
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  negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
@@ -145,88 +145,88 @@
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  </li>
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  <li>
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  <li>
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- <pre><%= ERB::Util.h %q|-taxids <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-taxids <String>
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  Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',')
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  * Incompatible with: gilist, seqidlist, taxidlist, negative_gilist,
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
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  subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-negative_taxids <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_taxids <String>
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  Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',')
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  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
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  negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
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  subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-taxidlist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-taxidlist <String>
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  Restrict search of database to include only the specified taxonomy IDs
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  * Incompatible with: gilist, seqidlist, taxids, negative_gilist,
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  negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
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  subject_loc| %></pre>
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  </li>
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  <li>
169
- <pre><%= ERB::Util.h %q|-negative_taxidlist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-negative_taxidlist <String>
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  Restrict search of database to everything except the specified taxonomy IDs
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  * Incompatible with: gilist, seqidlist, taxids, taxidlist,
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  negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
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  subject_loc| %></pre>
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  </li>
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  <li>
176
- <pre><%= ERB::Util.h %q| -ipglist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -ipglist <String>
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  Restrict search of database to list of IPGs
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  * Incompatible with: subject, subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q| -negative_ipglist <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q| -negative_ipglist <String>
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  Restrict search of database to everything except the specified IPGs
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  * Incompatible with: subject, subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-entrez_query <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-entrez_query <String>
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  Restrict search with the given Entrez query
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  * Requires: remote| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-db_soft_mask <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-db_soft_mask <String>
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  Filtering algorithm ID to apply to the BLAST database as soft masking
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  * Incompatible with: db_hard_mask, subject, subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-db_hard_mask <String>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-db_hard_mask <String>
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  Filtering algorithm ID to apply to the BLAST database as hard masking
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  * Incompatible with: db_soft_mask, subject, subject_loc| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-qcov_hsp_perc <Real, 0..100>
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  Percent query coverage per hsp| %></pre>
203
203
  </li>
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  <li>
205
- <pre><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
205
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-max_hsps <Integer, >=1>
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  Set maximum number of HSPs per subject sequence to save for each query| %></pre>
207
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  </li>
208
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  <li>
209
- <pre><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-culling_limit <Integer, >=0>
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  If the query range of a hit is enveloped by that of at least this
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  many higher-scoring hits, delete the hit
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  * Incompatible with: best_hit_overhang, best_hit_score_edge| %></pre>
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  </li>
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  <li>
215
- <pre><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-best_hit_overhang <Real, (>0 and <0.5)>
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  Best Hit algorithm overhang value (recommended value: 0.1)
217
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  * Incompatible with: culling_limit| %></pre>
218
218
  </li>
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  <li>
220
- <pre><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-best_hit_score_edge <Real, (>0 and <0.5)>
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  Best Hit algorithm score edge value (recommended value: 0.1)
222
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  * Incompatible with: culling_limit| %></pre>
223
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-subject_besthit
225
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-subject_besthit
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  Turn on best hit per subject sequence| %></pre>
227
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-max_target_seqs <Integer, >=1>
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  Maximum number of aligned sequences to keep (value of 5 or more is recommended)
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  Default = '500'
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  * Incompatible with: num_descriptions, num_alignments| %></pre>
@@ -235,54 +235,54 @@
235
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236
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  <br/>
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238
- <h5>Statistical options</h5>
239
- <ul class="list-unstyled">
238
+ <h5 class="text-lg py-4 font-medium">Statistical options</h5>
239
+ <ul class="list-unstyled space-y-2">
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  <li>
241
- <pre><%= ERB::Util.h %q|-dbsize <Int8>
241
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-dbsize <Int8>
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  Effective length of the database| %></pre>
243
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-searchsp <Int8, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-searchsp <Int8, >=0>
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  Effective length of the search space| %></pre>
247
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  </li>
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  </ul>
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  <br/>
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252
- <h5>Extension options</h5>
253
- <ul class="list-unstyled">
252
+ <h5 class="text-lg py-4 font-medium">Extension options</h5>
253
+ <ul class="list-unstyled space-y-2">
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  <li>
255
- <pre><%= ERB::Util.h %q|-xdrop_ungap <Real>
255
+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-xdrop_ungap <Real>
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  X-dropoff value (in bits) for ungapped extensions| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-xdrop_gap <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-xdrop_gap <Real>
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  X-dropoff value (in bits) for preliminary gapped extensions| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-xdrop_gap_final <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-xdrop_gap_final <Real>
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  X-dropoff value (in bits) for final gapped alignment| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-window_size <Integer, >=0>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-window_size <Integer, >=0>
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  Multiple hits window size, use 0 to specify 1-hit algorithm| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-ungapped
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-ungapped
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  Perform ungapped alignment only?| %></pre>
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  </li>
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  </ul>
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  <br/>
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- <h5>Miscellaneous options</h5>
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- <ul class="list-unstyled">
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+ <h5 class="text-lg py-4 font-medium">Miscellaneous options</h5>
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+ <ul class="list-unstyled space-y-2">
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  <li>
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- <pre><%= ERB::Util.h %q|-parse_deflines <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-parse_deflines <Real>
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  Should the query and subject defline(s) be parsed?| %></pre>
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  </li>
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  <li>
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- <pre><%= ERB::Util.h %q|-use_sw_tback <Real>
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+ <pre class="bg-gray-100 border rounded overflow-x-auto p-2 font-mono hover:bg-yellow-100"><%= ERB::Util.h %q|-use_sw_tback <Real>
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  Compute locally optimal Smith-Waterman alignments?| %></pre>
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  </li>
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-
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+
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  </ul>