-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbbtmstool_blastup.php
239 lines (216 loc) · 9.27 KB
/
bbtmstool_blastup.php
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
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1" />
<link REL="SHORTCUT ICON" HREF="favicon.ico">
<link rel="stylesheet" type="text/css" href="css/stylebbtmst.css">
<meta name="description" content="Beta Barrel TransMembrane (BBTM) Search Tool (BBTM-ST)">
<meta name="keywords" content="beta,barrel,transmembrane,membrane,search,tool,bioinformatics,PLoS,one">
<meta name="author" content="David Jimenez-Morales">
<title>beta barrel TransMembrane Segment Search Tool</title>
<SCRIPT TYPE="text/javascript">
<!--
function dropdown(mySel)
{
var myWin, myVal;
myVal = mySel.options[mySel.selectedIndex].value;
if(myVal)
{
if(mySel.form.target)myWin = parent[mySel.form.target];
else myWin = window;
if (! myWin) return true;
myWin.location = myVal;
}
return false;
}
function MM_jumpMenu(targ,selObj,restore){ //v3.0
eval(targ+".location='"+selObj.options[selObj.selectedIndex].value+"'");
if (restore) selObj.selectedIndex=0;
}
function MM_findObj(n, d) { //v4.01
var p,i,x; if(!d) d=document; if((p=n.indexOf("?"))>0&&parent.frames.length) {
d=parent.frames[n.substring(p+1)].document; n=n.substring(0,p);}
if(!(x=d[n])&&d.all) x=d.all[n]; for (i=0;!x&&i<d.forms.length;i++) x=d.forms[i][n];
for(i=0;!x&&d.layers&&i<d.layers.length;i++) x=MM_findObj(n,d.layers[i].document);
if(!x && d.getElementById) x=d.getElementById(n); return x;
}
function MM_jumpMenuGo(selName,targ,restore){ //v3.0
var selObj = MM_findObj(selName); if (selObj) MM_jumpMenu(targ,selObj,restore);
}
//-->
</SCRIPT>
<!--STATS-->
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-26635029-1', 'auto');
ga('send', 'pageview');
</script>
<!--STATS-->
</head>
<body>
<table width="650" border="0" align="center" cellpadding="0" cellspacing="0">
<tr>
<td><a name="top" id="top"></a></td>
</tr>
<tr>
<td><table width="98%" border="0" align="center" cellpadding="0" cellspacing="0">
<tr>
<td width="25%"><a href="http://www.uic.edu/uic/" target="_blank" class="style4">UIC</a></td>
<td width="45%"><div align="center"><a href="http://gila.bioe.uic.edu/lab/" target="_blank" class="style4">Jie Liang Lab</a></div></td>
<td width="30%"><div align="right"><a href="http://gila.bioe.uic.edu/lab/" target="_blank"></a><a href="http://www.bioe.uic.edu/BIOE/WebHome" target="_blank" class="style4">Department of Bioengineering</a></div></td>
</tr>
</table></td>
</tr>
<tr>
<td> </td>
</tr>
<tr>
<td><table width="98%" border="0" align="center" cellpadding="0" cellspacing="0">
<tr>
<td width="42%"><div align="center"><img src="images/logowhite.jpg" width="158" height="100" /></div></td>
<!-- <td width="58%"><p class="style8">bbTM-ST<br /> -->
<td width="58%"><h1 class="h1title">bbTM-ST</h1>
<span class="style7">β-Barrel TransMembrane Search Tool</span></p> </td>
</tr>
</table></td>
</tr>
<tr>
<td> </td>
</tr>
<tr>
<td >
<div class="submenu">
<span class="style22">
<a href="index.html">Main</a> ·
<a href="bbtmstool.php">BBTM-SearchTool</a>
</span>
</div>
</td>
</tr>
<tr>
<td>
<p class="descriptor"><span ><strong>BLAST</strong> searches using the <strong>bbTM</strong> scoring matrices<br/> against the <strong>NR-NCBI database</strong>.</span></p>
</td>
</tr>
<tr>
<td height="26"><p><strong>><em>Transmembrane fragment search for structures of beta barrel membrane proteins with a solved structure using the bbTMout matrix: </em></strong></p> </td>
</tr>
<tr>
<td><form id="form1" name="form1">
<label>List of PDBs</label>
<select name="PDB-SELECT" onchange="MM_jumpMenu('parent',this,0)">
<option>Select a beta barrel PDB:</option>
<option value="supmat/blast2nr/in1A0S.blast2nr.bbTMout">1A0S</option>
<option value="supmat/blast2nr/in1BXW.blast2nr.bbTMout">1BXW</option>
<option value="supmat/blast2nr/in1E54.blast2nr.bbTMout">1E54</option>
<option value="supmat/blast2nr/in1EK9.blast2nr.bbTMout">1EK9</option>
<option value="supmat/blast2nr/in1FEP.blast2nr.bbTMout">1FEP</option>
<option value="supmat/blast2nr/in1I78.blast2nr.bbTMout">1I78</option>
<option value="supmat/blast2nr/in1K24.blast2nr.bbTMout">1K24</option>
<option value="supmat/blast2nr/in1KMO.blast2nr.bbTMout">1KMO</option>
<option value="supmat/blast2nr/in1NQE.blast2nr.bbTMout">1NQE</option>
<option value="supmat/blast2nr/in1P4T.blast2nr.bbTMout">1P4T</option>
<option value="supmat/blast2nr/in1PRN.blast2nr.bbTMout">1PRN</option>
<option value="supmat/blast2nr/in1QD6.blast2nr.bbTMout">1QD6</option>
<option value="supmat/blast2nr/in1QJ8.blast2nr.bbTMout">1QJ8</option>
<option value="supmat/blast2nr/in1T16.blast2nr.bbTMout">1T16</option>
<option value="supmat/blast2nr/in1THQ.blast2nr.bbTMout">1THQ</option>
<option value="supmat/blast2nr/in1XKW.blast2nr.bbTMout">1XKW</option>
<option value="supmat/blast2nr/in2F1C.blast2nr.bbTMout">2F1C</option>
<option value="supmat/blast2nr/in2FCP.blast2nr.bbTMout">2FCP</option>
<option value="supmat/blast2nr/in2MPR.blast2nr.bbTMout">2MPR</option>
<option value="supmat/blast2nr/in2OMF.blast2nr.bbTMout">2OMF</option>
</select>
<input type="button" name="ButtonA" value="Go" onclick="MM_jumpMenuGo('PDB-SELECT','parent',0)" />
</form></td>
</tr>
<tr> </tr>
<tr>
<td> </td>
</tr>
<tr>
<td height="26"><p><strong>><em>Transmembrane fragment search for human mitochondrial beta-barrel membrane proteins: </em></strong></p> </td>
</tr>
<tr>
<td><form id="form2" name="form2">
<label>List of mitochondrial proteins / bbTM matrices:</label>
<select name="MITO-SELECT" onchange="MM_jumpMenu('parent',this,0)">
<option>Select a BLAST output</option>
<option value="supmat/blast2nr/inVDAC1hum.blast2nr.bbTMout">VDAC1.bbTMout</option>
<option value="supmat/blast2nr/inVDAC1hum.blast2nr.bbTMin">VDAC1.bbTMin</option>
<option value="supmat/blast2nr/inVDAC1hum.blast2nr.bbTMall">VDAC1.bbTMall</option>
<option value="supmat/blast2nr/inSAM50hum.blast2nr.bbTMout">SAM50.bbTMout</option>
<option value="supmat/blast2nr/inSAM50hum.blast2nr.bbTMin">SAM50.bbTMin</option>
<option value="supmat/blast2nr/inSAM50hum.blast2nr.bbTMall">SAM50.bbTMall</option>
<option value="supmat/blast2nr/inTOM40hum.blast2nr.bbTMout">TOM40.bbTMout</option>
<option value="supmat/blast2nr/inTOM40hum.blast2nr.bbTMin">TOM40.bbTMin</option>
<option value="supmat/blast2nr/inTOM40hum.blast2nr.bbTMall">TOM40.bbTMall</option>
</select>
<input type="button" name="ButtonB" value="Go" onclick="MM_jumpMenuGo('MITO-SELECT','parent',0)" />
</form></td>
</tr>
<tr> </tr>
<tr>
<td></td>
</tr>
<tr>
<td height="25"> </td>
</tr>
<tr>
<td><p><strong>> Provide your own transmembrane segment. <br />
</strong> Minimal sequence length: 20 amino acids. FASTA format required. Example of FASTA format:</p>
<blockquote>
<p>>name of the sequence<br />
AMINQACIDSEQAENCETRANSMEMIRANESEGMENTS</p>
</blockquote></td>
</tr>
<tr>
</tr>
<?php if ($_GET["val"] == "fail") { ?>
<tr>
<td><span class="error"><?echo $_GET["error"]; ?> - Invalid Fasta Sequence
</span><form action="scripts/fproc.php" method ="post">
<textarea rows="8" cols="50" wrap="physical" name="fasta" /></textarea>
<input type="submit" value="Submit again"></form> </td>
</form> </td>
</tr>
<?php } elseif ($_GET["val"] == "true") { ?>
<tr>
<td><span class="fasta">BLAST results are ready:</span>
<br><a href="<?echo $_GET['file']?>" target="_blank">Download Results</a>
<form name="ClearFile" action="bbtmstool.php">
<input type="submit" value="Clear File and refresh page"></form> </td>
</tr>
<?php } else { ?>
<tr>
<td>
<div class="hideme" id="waiting">
<p class="styleWaiting"> Job submitted: please be patient while BLAST runs</p>
<p>(The <strong>NCBI non-redundant database</strong> is very large... and our computational power very limited)</p>
</div>
<form action="scripts/fproc.php" method ="post">
<textarea rows="8" cols="50" wrap="physical" name="fasta" /></textarea>
<input onclick="document.getElementById('waiting').className='showme';" type="submit" value="Submit">
</form> </td>
</tr>
<?php } ?>
<tr>
<td> </td>
</tr>
<tr>
<td> </td>
</tr>
<tr>
<td height="23"><div align="center"><strong>David Jimenez-Morales and Jie Liang </strong></div></td>
</tr>
<tr>
<td><p align="center" class="style4">Dept of Bioengineering/ Bioinformatics Program<br />
<span class="style3">University of Illinois at Chicago</span><br />
<span class="style6">Chicago, Illinois, United States of America</span></p> </td>
</tr>
</table>
</body>
</html>