-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathblast.php
More file actions
197 lines (182 loc) · 8.28 KB
/
blast.php
File metadata and controls
197 lines (182 loc) · 8.28 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
<?php
isset($_POST['qtitle']) && $_POST['qtitle']?$qtitle=$_POST['qtitle']:$qtitle='';
isset($_POST['qs']) && $_POST['qs']?$qs=$_POST['qs']:$qs='';
?>
<?php
include("template.php");
echoHtmlHead("Blast submition");
?>
<link href="css/blast.css" rel="stylesheet" type="text/css" />
<script type="text/javascript" src="js/blast.js"></script>
<?php echoPageHeader(); ?>
<!-- ================================== main content start ===================================== -->
<div id="main">
<form action='remote.php' method="post" name="blast" id="blast" class="blast" enctype="multipart/form-data">
<table width="960" border="0">
<tr>
<th scope="col">Enter Query Sequence<em>FASTA format</em></th>
<td><textarea id="query" class="reset" rows="5" cols="80" name="QUERY" onblur="checkSeqFormat(this)"><?php echo $qs; ?></textarea><span class="button"><a href="#" onclick="clearSeq('query')">clear</a></span></td>
</tr>
<tr>
<th scope="row">Or, upload file</th>
<td><input id="upl" name="QUERYFILE" type="file" size="70"></td>
</tr>
<tr>
<th scope="row">Job Title</th>
<td><?php echo "<input name=\"JOB_TITLE\" id=\"qtitle\" class=\"reset\" size=\"80\" value=\"$qtitle\">"; ?></td>
</tr>
<tr>
<td><input name="BL2SEQ" value="y" id="bl2seq" type="checkbox" onclick="toggle(['sseq','db']);">
<label>Align two sequences</label></td>
<td></td>
</tr>
</table>
<div id="sseq" class="collapse">
<table width="960" border="0" >
<tr>
<th scope="row">Enter Subject Sequence<em>FASTA format</em></th>
<td><textarea id="subject" class="reset" rows="5" cols="80" name="SUBJECT" onblur="checkSeqFormat(this)"></textarea><span class="button"><a href="#" onclick="clearSeq('subject')">clear</a></span></td>
</tr>
<tr>
<th scope="row">Or, upload file</th>
<td><input id="up2" name="SUBJECTFILE" type="file" size="70"></td>
</tr>
</table>
</div>
<table width="960" border="0">
<tr>
<th scope="row">Program</th>
<td><select name="PROGRAM" id="program" class="reset checkDef" onchange="setPara(this)">
<option id="Ohc" value="blastn" selected="selected">blastn</option>
<option id="Omc" value="blastp">blastp</option>
<option id="Omc" value="blastx">blastx</option>
<option id="Omc" value="tblastn">tblastn</option>
<option id="Omc" value="tblastx">tblastx</option>
</select>
</td>
</tr>
<tr id="db" class="expand">
<th scope="row">Database</th>
<td><select name="DATABASE" id="database" class="reset checkDef">
<option id="Ohc" value="clostridium" selected="selected">clostridium</option>
<option id="Omc" value="nr">nr</option>
</select>
</td>
</tr>
</table>
<div class="button toggle"><a href="#" onclick="toggle(['para'])">Parameters Setting</a></div>
<div id="para" class="collapse">
<table width="960" border="0">
<tr>
<th scope="row">Max target sequences</th>
<td><select name="MAX_NUM_SEQ" class="reset checkDef opts" id="NUM_SEQ" defval="100">
<option value="10">10</option>
<option value="50">50</option>
<option value="100" selected="selected">100</option>
<option value="250">250</option>
<option value="500">500</option>
<option value="1000">1000</option>
<option value="5000">5000</option>
<option value="10000">10000</option>
<option value="20000">20000</option>
</select>
</td>
</tr>
<tr>
<th scope="row">Expect threshold</th>
<td><input name="EXPECT" id="expect" class="reset checkDef opts" size="10" value="10" defval="10" type="text">
</td>
</tr>
<tr>
<th scope="row">Word size</th>
<td><select name="WORD_SIZE" id="wordsize" class="reset checkDef opts" defval="11">
<option value="7">7</option>
<option value="11" class="Deflt" selected="selected">11</option>
<option value="15">15</option>
</select>
</td>
</tr>
<tr id="code" class="collapse">
<th scope="row">Genetic code</th>
<td>
<select name="GENETIC_CODE" class="reset" id="GENETIC_CODE">
<option value="1" >Standard (1)</option>
<option value="2" >Vertebrate Mitochondrial (2)</option>
<option value="3" >Yeast Mitochondrial (3)</option>
<option value="4" >Mold Mitochondrial; ... (4)</option>
<option value="5" >Invertebrate Mitochondrial (5)</option>
<option value="6" >Ciliate Nuclear; ... (6)</option>
<option value="9" >Echinoderm Mitochondrial (9)</option>
<option value="10" >Euplotid Nuclear (10)</option>
<option value="11" >Bacteria and Archaea (11)</option>
<option value="12" >Alternative Yeast Nuclear (12)</option>
<option value="13" >Ascidian Mitochondrial (13)</option>
<option value="14" >Flatworm Mitochondrial (14)</option>
<option value="15" >Blepharisma Macronuclear (15)</option>
</select>
</td>
</tr>
<tr id="matrix" class="collapse">
<th scope="row">Matrix</th>
<td><select name="MATRIX_NAME" id="matrixName" class="reset checkDef opts" defval="">
<option value="PAM30">PAM30</option>
<option value="PAM70">PAM70</option>
<option value="BLOSUM80">BLOSUM80</option>
<option value="BLOSUM62" selected="selected">BLOSUM62</option>
<option value="BLOSUM45">BLOSUM45</option>
</select>
</td>
</tr>
<tr id="match" class="collapse">
<th scope="row">Match/Mismatch Scores</th>
<td><select name="MATCH_SCORES" id="matchscores" class="reset checkDef opts" defval="2,-3">
<option value="1,-2">1,-2</option>
<option value="1,-3">1,-3</option>
<option value="1,-4">1,-4</option>
<option value="2,-3" selected="selected">2,-3</option>
<option value="4,-5">4,-5</option>
<option value="1,-1">1,-1</option>
</select>
</td>
</tr>
<tr id="gap" class="collapse">
<th scope="row">Gap Costs</th>
<td><select name="GAPCOSTS" id="gapcosts" class="reset checkDef opts" defval="5 2">
<option value="4 4">Existence: 4 Extension: 4</option>
<option value="2 4">Existence: 2 Extension: 4</option>
<option value="0 4">Existence: 0 Extension: 4</option>
<option value="3 3">Existence: 3 Extension: 3</option>
<option value="6 2">Existence: 6 Extension: 2</option>
<option selected="selected" value="5 2">Existence: 5 Extension: 2</option>
<option value="4 2">Existence: 4 Extension: 2</option>
<option value="2 2">Existence: 2 Extension: 2</option>
</select>
</td>
</tr>
<tr id="compo" class="collapse">
<th scope="row">Compositional adjustments</th>
<td><select name="COMPOSITION_BASED_STATISTICS" id="compbasedstat" class="reset checkDef opts" defval="2">
<option value="0">No adjustment</option>
<option value="1">Composition-based statistics</option>
<option value="2" selected="selected">Conditional compositional score matrix adjustment</option>
<option value="3">Universal compositional score matrix adjustment</option>
</select>
</td>
</tr>
<tr>
<th scope="row">Filter</th>
<td><input name="FILTER" value="T" id="fil_l" checked="checked" class="reset checkDef opts" defval="checked" type="checkbox">
<label class="right inlinelabel" for="fil_l">Low complexity regions <span class="acPromt">filter</span></label> </td>
</tr>
<tr>
<th scope="row">Mask</th>
<td><input name="MASK" value="m" id="fil_m" checked="checked" class="reset checkDef opts" defval="checked" type="checkbox">
<label class="right inlinelabel" for="fil_m">Mask for lookup table only</label></td>
</tr>
</table>
</div>
<input name="" type="button" class="go" value="BLAST" onclick="runblast()" />
</form>
</div>
<!-- =================================== main content end ======================================== -->
<?php echoPageFooter(); ?>