<%args>
$sequenceset_html => undef
$organism_html => undef
$sequence_input => undef
$admin => 0
$sequence_data_dir
</%args>
<script type="text/javascript" src="/js/mimosa-grid.js"></script>
<div id="tabs1">
<div id="t1_content">
<div id="pagetitle">
<h2>Mimosa - Miniature Model Organism Sequence Aligner</h2>
</div>
<div id="mimosa-grid">
</div>
<table border="0">
<form method="post" enctype="multipart/form-data" action="/submit" name="main_input_form">
<input type="hidden" id="mimosa_sequence_set_ids" name="mimosa_sequence_set_ids" value="0" />
<input type="hidden" name="interface_type" value="simple" />
<input type="hidden" name="outformat" value="0" />
<br>
<tr><td>
Program:</td><td> <select id="program_selector" name="program">
<option value="none">Choose a BLAST program</option>
<option selected="true" value="blastn">BLASTN (nucleotide to nucleotide)</option>
<option value="tblastx">TBLASTX (protein to protein; both database and query are translated)</option>
<option value="tblastn">TBLASTN (protein to nucleotide; database translated to protein)</option>
</select>
</td></tr>
<tr><td>Name:</td><td> <input type="text" name="search_name" size="20" id="search_name"></td></tr>
<tr><td>Description:</td><td> <input type="text" name="search_description" size="20" id="search_description"></td></tr>
<tr><td><b>Query sequence</b></td></tr>
<tr><td colspan="2">
<textarea name="sequence" id="sequence_input" rows="8" cols="80"><% $sequence_input %></textarea></td></tr>
<tr><td>Upload query sequence file:</td><td> <input type="file" name="sequence_input_file" size="40"></td></tr>
</table>
<br/>
<input value="unchecked" type="checkbox" name="advanced" id="advanced_control" onclick="$('#advanced').toggle('slow', 'swing')">
<label for="advanced_control">Advanced Options</label>
<div class="info_table_fieldval">
<div id="advanced" style="display:none; width: 700px;">
Filter Query?: <input type="checkbox" checked="checked" name="filtered" value="T" /><br/>
<div class="info_table_fieldval">
Expect (e-value) Threshold
<input type="text" size="6" value="1e-10" name="evalue" />
<br/>
</div>
<div>
Alignment View
<select id="alignment_views" name="alignment_view">
<option value="0">Pairwise</option>
<option value="1">Query-anchored showing identities</option>
<option value="2">Query-anchored no identities</option>
<option value="3">Flat query-anchored, show identities</option>
<option value="4">Flat query-anchored, no identities</option>
<option value="5">Query-anchored no identities and blunt ends</option>
<option value="6">Flat query-anchored, no identities and blunt ends</option>
<option value="7">XML Blast output</option>
<option value="8">Tabular</option>
<option value="9">Tabular with comment lines</option>
<option value="10">ASN text</option>
</select>
</div>
<div class="info_table_fieldval">
Substitution Matrix
<select id="simple_selectbox_2" name="matrix">
<option value="BLOSUM62">BLOSUM62 (default)</option>
<option value="BLOSUM80">BLOSUM80 (recent divergence)</option>
<option value="BLOSUM45">BLOSUM80 (ancient divergence)</option>
<option value="PAM30">PAM30</option>
<option value="PAM70">PAM70</option>
</select>
</div>
<div class="info_table_fieldval">
Show Graphics
<select id="simple_selectbox_3" name="output_graphs">
<option value="bioperl_histogram">all</option>
<option value="none">none</option>
<option value="bioperl_only">alignment summary only</option>
</select>
</div>
<div class="info_table_fieldval">
Max hits to show: <input type="text" name="maxhits" size="6" value="100" />
</div>
</div> <!-- advanced -->
<div><br/><input type="reset" value="Clear" onclick="clearField(); "> <input type="submit" name="search" value="Align" ></div>
</div>
</form>
</div> <!-- t1_content -->
<& tabs.mason, sequence_data_dir => $sequence_data_dir &>
</div>