EOL/seabase

%form{:action => "/blast", :enctype => "multipart/form-data", :method => "POST", :name => "MainBlastForm"}
  %b Choose program to use and database to search:
  %p
    %a{:href => "docs/blast_program.html"} Program
    %select{:name => "PROGRAM"}
      %option
        blastn
      %option
        blastp
      %option
        blastx
      %option
        tblastn
      %option
        tblastx
    %a{:href => "docs/blast_databases.html"} Database
    %select{:name => "DATALIB"}
      %option{:value => "nematostella_vectensis_transcriptome"}
        nematostella vectensis transcriptome
  %p
    Enter sequence below in
    %a{:href => "docs/fasta.html"} FASTA
    format
    %br/
    %textarea{:cols => "60", :name => "SEQUENCE", :rows => "6"}
    %br/
    Or load it from disk
    %input{:name => "SEQFILE", :type => "file"}/
  %p
    Set subsequence: From
    \ &nbsp
    %input{:name => "QUERY_FROM", :size => "10", :type => "text", :value => ""}/
    \ &nbsp &nbsp To
    %input{:name => "QUERY_TO", :size => "10", :type => "text", :value => ""}/
  %p
    %input{:onclick => "MainBlastForm.SEQUENCE.value='';MainBlastForm.QUERY_FROM.value='';MainBlastForm.QUERY_TO.value='';MainBlastForm.SEQUENCE.focus();", :type => "button", :value => "Clear sequence"}/
    %input{:type => "submit", :value => "Run Blast", :id => "run_blast_1"}/
  %hr/
  The query sequence is
  %a{:href => "docs/filtered.html"} filtered
  for low complexity regions by default.
  %br/
  %a{:href => "docs/newoptions.html#filter"} Filter
  %input{:checked => "", :name => "FILTER", :type => "checkbox", :value => "L"}/
  Low complexity
  %input{:name => "FILTER", :type => "checkbox", :value => "m"}/
  Mask for lookup table only
  %p
    %a{:href => "docs/newoptions.html#expect"} Expect
    %select{:name => "EXPECT"}
      %option
        0.0001
      %option
        0.01
      %option
        1
      %option{:selected => ""}
        10
      %option
        100
      %option
        1000
    \  
    %a{:href => "docs/matrix_info.html"} Matrix
    %select{:name => "MAT_PARAM"}
      %option{:value => "PAM30\t 9\t 1"} PAM30
      %option{:value => "PAM70\t 10\t 1"} PAM70
      %option{:value => "BLOSUM80\t 10\t 1"} BLOSUM80
      %option{:selected => "", :value => "BLOSUM62\t 11\t 1"} BLOSUM62
      %option{:value => "BLOSUM45\t 14\t 2"} BLOSUM45
    %input{:name => "UNGAPPED_ALIGNMENT", :type => "checkbox", :value => "is_set"}/
    Perform ungapped alignment
  %p
    %a{:href => "docs/newoptions.html#gencodes"}
      Query Genetic Codes (blastx only)
    %select{:name => "GENETIC_CODE"}
      %option
        Standard (1)
      %option
        Vertebrate Mitochondrial (2)
      %option
        Yeast Mitochondrial (3)
      %option
        Mold Mitochondrial; ... (4)
      %option
        Invertebrate Mitochondrial (5)
      %option
        Ciliate Nuclear; ... (6)
      %option
        Echinoderm Mitochondrial (9)
      %option
        Euplotid Nuclear (10)
      %option
        Bacterial (11)
      %option
        Alternative Yeast Nuclear (12)
      %option
        Ascidian Mitochondrial (13)
      %option
        Flatworm Mitochondrial (14)
      %option
        Blepharisma Macronuclear (15)
  %p
    %a{:href => "docs/newoptions.html#gencodes"}
      Database Genetic Codes (tblast[nx] only)
    %select{:name => "DB_GENETIC_CODE"}
      %option
        Standard (1)
      %option
        Vertebrate Mitochondrial (2)
      %option
        Yeast Mitochondrial (3)
      %option
        Mold Mitochondrial; ... (4)
      %option
        Invertebrate Mitochondrial (5)
      %option
        Ciliate Nuclear; ... (6)
      %option
        Echinoderm Mitochondrial (9)
      %option
        Euplotid Nuclear (10)
      %option
        Bacterial (11)
      %option
        Alternative Yeast Nuclear (12)
      %option
        Ascidian Mitochondrial (13)
      %option
        Flatworm Mitochondrial (14)
      %option
        Blepharisma Macronuclear (15)
  %p
    %a{:href => "docs/oof_notation.html"} Frame shift penalty
    for blastx
    %select{:name => "OOF_ALIGN"}
      %option
        6
      %option
        7
      %option
        8
      %option
        9
      %option
        10
      %option
        11
      %option
        12
      %option
        13
      %option
        14
      %option
        15
      %option
        16
      %option
        17
      %option
        18
      %option
        19
      %option
        20
      %option
        25
      %option
        30
      %option
        50
      %option
        1000
      %option{:selected => "", :value => "0"}
        No OOF
  %p
    %a{:href => "docs/full_options.html"} Other advanced options:
    \    
    %input{:maxlength => "50", :name => "OTHER_ADVANCED", :type => "text", :value => ""}/
  %hr/
  /
    <INPUT TYPE="checkbox" NAME="NCBI_GI" >&amp;nbsp;&amp;nbsp;
    <a href="docs/newoptions.html#ncbi-gi"> NCBI-gi</a>
    \&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;
  %input{:checked => "", :name => "OVERVIEW", :type => "checkbox"}/
  %a{:href => "docs/newoptions.html#graphical-overview"} Graphical Overview
  \&nbsp;&nbsp;
  %a{:href => "docs/options.html#alignmentviews"} Alignment view
  %select{:name => "ALIGNMENT_VIEW"}
    %option{:value => "0"}
      Pairwise
    %option{:value => "1"}
      master-slave with identities
    %option{:value => "2"}
      master-slave without identities
    %option{:value => "3"}
      flat master-slave with identities
    %option{:value => "4"}
      flat master-slave without identities
    %option{:value => "7"}
      BLAST XML
    %option{:value => "9"}
      Hit Table
  %br/
  %a{:href => "docs/newoptions.html#descriptions"} Descriptions
  %select{:name => "DESCRIPTIONS"}
    %option
      0
    %option
      10
    %option
      50
    %option{:selected => ""}
      100
    %option
      250
    %option
      500
  \&nbsp;&nbsp;
  %a{:href => "docs/newoptions.html#alignments"} Alignments
  %select{:name => "ALIGNMENTS"}
    %option
      0
    %option
      10
    %option{:selected => ""}
      50
    %option
      100
    %option
      250
    %option
      500
  %a{:href => "docs/color_schema.html"} Color schema
  %select{:name => "COLOR_SCHEMA"}
    %option{:selected => "", :value => "0"}
      No color schema
    %option{:value => "1"}
      Color schema 1
    %option{:value => "2"}
      Color schema 2
    %option{:value => "3"}
      Color schema 3
    %option{:value => "4"}
      Color schema 4
    %option{:value => "5"}
      Color schema 5
    %option{:value => "6"}
      Color schema 6
  %p
    %input{:onclick => "MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQFILE.value='';MainBlastForm.SEQUENCE.focus();", :type => "button", :value => "Clear sequence"}/
    %input{:type => "submit", :value => "Run Blast", :id => 'run_blast_2'}/