-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathprediction.html
executable file
·362 lines (332 loc) · 20.2 KB
/
prediction.html
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
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>LegumeLoc - Prediction</title>
<link href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-rbsA2VBKQhggwzxH7pPCaAqO46MgnOM80zW1RWuH61DGLwZJEdK2Kadq2F9CUG65" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/font/bootstrap-icons.css">
<link href="assets/css/style.css" rel="stylesheet">
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js" integrity="sha384-kenU1KFdBIe4zVF0s0G1M5b4hcpxyD9F7jL+jjXkk+Q2h455rYXK/7HAuoJl+0I4" crossorigin="anonymous"></script>
<script type="text/javascript" language="javascript" src="https://code.jquery.com/jquery-3.5.1.js"></script>
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-QWCEDDGJN3"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-QWCEDDGJN3');
</script>
</head>
<body>
<header>
<nav class="navbar navbar-dark navbar-expand-lg bd-navbar">
<div class="container">
<a class="navbar-brand bd-brand" href="index.html">LegumeLoc</a>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse"
data-bs-target="#navbarNavAltMarkup" aria-controls="navbarNavAltMarkup" aria-expanded="false"
aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse justify-content-center" id="navbarNavAltMarkup">
<div class="navbar-nav">
<a class="nav-link bd-link" aria-current="page" href="index.html"><i
class="bi bi-info-square-fill mx-2"></i><span>Home</span>
</a>
<a class="nav-link bd-link active" href="prediction.html"><i
class="bi bi-terminal-fill mx-2"></i><span>Prediction</span>
</a>
<a class="nav-link bd-link" href="download.html"><i
class="bi bi-cloud-arrow-down-fill mx-2"></i><span>Downloads</span>
</a>
<a class="nav-link bd-link" href="help.html"><i
class="bi bi-question-square-fill mx-2"></i><span>User guide</span>
</a>
</div>
</div>
</div>
</nav>
</header>
<div id= "mainc" class="container pt-4 t-3 mx-auto ">
<h2 class="fw-bold mb-2 mt-1 text-center">Submission</h2>
<div class="px-5 my-3 mb-4">
<div class="line" style="width: 100%;"></div>
</div>
<form action="" method="POST" enctype="multipart/form-data">
<div class="row mb-2 justify-content-center">
<div class="col-md-8">
<div class="row">
<p style="font-size: 18px; text-align: justify; margin-bottom: 30px;">
Enter NCBI/UniProt accession ID or paste/upload protein sequence(s) in FASTA format to predict the subcellular
localization. The prediction time depends on the model selected. A maximum of <b>10,000 protein sequences</b> are
allowed on this server.
</p>
<div class="col-sm-2">
<h6 class="mb-2 mt-2 text-head">
Accession ID:
</h6>
</div>
<div class="col-sm-9">
<div class="row">
<div class="col-sm-7">
<div class="form-check form-check-inline mt-2">
<input class="form-check-input" id="ncbiAccc" value="ncbi" name="accType"
checked="" type="radio"><label for="ncbiAccc"
class="form-check-label ptext px-2 ">NCBI</label>
</div>
<div class="form-check form-check-inline mt-2">
<input class="form-check-input" id="uniprotAcc" value="uniprot" name="accType"
type="radio"><label for="uniprotAcc"
class="form-check-label ptext px-2 ">UniProt</label>
</div>
</div>
<div class="col-sm-5">
<input class="form-control AtSubP2-form" placeholder="NP_001240185, Q6PSU2" name="accesion"
type="text" id="ncbiAcc">
</div>
</div>
</div>
<div class="col-md-12 my-4 col-title2 mt-3 mb-3">
OR
</div>
<div class="col-md-4 ptext text-head mt-1">
Upload a FASTA file:
</div>
<div class="col-sm-6">
<div class="input-group mb-2">
<input class="AtSubP2-from form-control" placeholder="Upload file here">
<input type="file" class="form-control-file real-input" name="fileSeq" id="fileSeq" />
<label class="btn AtSubP2-btn-1" for="fileSeq">Choose file</label>
</div>
</div>
<div class="col-md-12 my-4 col-title2 mt-3 mb-3">
OR
</div>
<div class="col-md-6 ptext text-head mt-2">
Paste FASTA sequence:
</div>
<div class="col-sm-6 mb-1">
<button type="button" id="loadDemoData" class="AtSubP2-btn-1 btn btn-primary">Load example</button>
</div>
<div class="col-md-12 mt-3">
<textarea class="AtSubP2-form form-control " id="textareaSeq" name="textareaSeq"
placeholder=">A0A191UJB7
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDDFLSVRVYLWHETTRSMGLAY"
rows="5"></textarea></p>
</div>
</div>
</div>
<div class="col-md-9 px-5 mt-4">
<div class="prediction-options-bar">
<h5 class="fw-bold mb-3 text-center">Prediction Options</h5>
</div>
<div class="row">
<div class="col-md-6">
<h6 class="text-head mb-2">
<p class="text-muted2 ms-3"> Select prediction level <i class="ms-2 bi bi-info-circle"
data-bs-toggle="modal" data-bs-target="#predictionModal"></i></p>
</h6>
<div class="form-check mx-4">
<input class="form-check-input mb-2 mx-2" id="phase1radio" value="Phase1" type="checkbox"
name="phase1radio">
<label class="form-check-label ltext" for="phase1radio">
Single vs Dual Localization Classification
</label>
</div>
<div class="form-check mx-4">
<input class="form-check-input mb-2 mx-2" id="phase2radio" value="Phase2" type="checkbox"
name="phase2radio">
<label class="form-check-label ltext" for="phase2radio">
Single Localization Classification
</label>
</div>
<div class="form-check mx-4">
<input class="form-check-input mb-2 mx-2" id="phase3radio" value="Phase3" type="checkbox"
name="phase3radio">
<label class="form-check-label ltext" for="phase3radio">
Dual Localization Classification
</label>
</div>
</div>
<div class="col-md-6">
<h6 class="text-head mb-0">
<p class="text-muted2 ms-3"> Select prediction model <i class="ms-2 bi bi-info-circle"
data-bs-toggle="modal" data-bs-target="#strategyModal"></i></p>
</h6>
<div class="row ms-5">
<div class="form-check form-check-inline col-md-3">
<input class="form-check-input" id="fastRadio" value="fast" name="predMethod" checked="" type="radio"><label
for="fastRadio" class="form-check-label ptext px-2 ">Fast</label>
</div>
<div class="form-check form-check-inline col-md-3">
<input class="form-check-input" id="accurateRadio" value="sensitive" name="predMethod" type="radio"><label
for="accurateRadio" class="form-check-label ptext px-2 ">Sensitive</label>
</div>
</div>
</div>
</div>
<hr>
<div class="col-md-10 mt-4 mb-4 form-group">
<h6 class="text-head mb-2">
<p class="text-muted2 ms-3"> Email address (Optional) </p>
</h6>
<input name="emailAddress" placeholder="Enter a valid email" class="AtSubP2-form form-control mt-2"
id="emailAddress" type="email" style="width: 70%; margin-left: 30px;">
</div>
</div>
<div class="px-5 my-5 mt-2 mb-3">
<div class="line " style="width: 100%;"></div>
</div>
<div class="row mx-auto justify-content-center ">
<div class="col-sm-4 mt-2 text-center">
<button type="button" id="resetPrediction" class="AtSubP2-btn-2 btn btn-primary">Reset All</button>
</div>
<div class="col-sm-4 mt-2 text-center">
<button id= "runPrediction" type="button" class="AtSubP2-btn-1 btn btn-primary"> Run Prediction</button>
</div>
</div>
</div>
</form>
<div class="modal fade" id="predictionModal" tabindex="-1" role="dialog" aria-labelledby="predictionModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title" id="predictionModalLabel">Prediction Levels</h5>
<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close">
</button>
</div>
<div class="modal-body">
<p style="font-size: 15px;">
<b>Level I</b>: The input protein sequence is predicted as single or dual localization class, based on the selected model.
</p>
<hr>
<p style="font-size: 15px;">
<b>Level II</b>: In this level, the query protein sequence predicted as single or dual localization is followed by the
prediction into 11 single localization classes as follows:
<ul style="columns: 2;">
<li style="font-size: 14px;">Vacuole</li>
<li style="font-size: 14px;">Cytoplasm</li>
<li style="font-size: 14px;">Peroxisome</li>
<li style="font-size: 14px;">Golgi apparatus</li>
<li style="font-size: 14px;">Endoplasmic Reticulum</li>
<li style="font-size: 14px;">Membrane</li>
<li style="font-size: 14px;">Secreted</li>
<li style="font-size: 14px;">Cell membrane</li>
<li style="font-size: 14px;">Mitochondria</li>
<li style="font-size: 14px;">Plastid</li>
<li style="font-size: 14px;">Nucleus</li>
</ul>
</p>
<hr>
<p style="font-size: 15px;">
<b>Level III</b>: This level will classify the proteins into 14 dual localization classes, which are:
<ul style="columns: 2;">
<li style="font-size: 14px;">CellMembrane & Membrane</li>
<li style="font-size: 14px;">Cytoplasm & Membrane</li>
<li style="font-size: 14px;">Cytoplasm & Mitochondria</li>
<li style="font-size: 14px;">Cytoplasm & Nucleus</li>
<li style="font-size: 14px;">Cytoplasm & Vesicle</li>
<li style="font-size: 14px;">Endoplasmic Reticulum & Membrane</li>
<li style="font-size: 14px;">Golgi apparatus & Membrane</li>
<li style="font-size: 14px;">Membrane & Mitochondria</li>
<li style="font-size: 14px;">Membrane & Nucleus</li>
<li style="font-size: 14px;">Membrane & Plastid</li>
<li style="font-size: 14px;">Membrane & Secreted</li>
<li style="font-size: 14px;">Membrane & Vacuole</li>
<li style="font-size: 14px;">Nucleus & Chromosome</li>
<li style="font-size: 14px;">Plastid & Mitochondria</li>
</ul>
</p>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-info" data-bs-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<div class="modal fade" id="strategyModal" tabindex="-1" role="dialog" aria-labelledby="strategyModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title font-weight-bold" id="strategyModalLabel">Prediction Strategy</h5>
<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<p style="font-size: 15px;">
LegumeLoc provides two prediction strategies:
</p>
<ul>
<li style="font-size: 14px;">
<b>Fast</b>: This model provides a faster prediction. This approach is useful in annotationg huge number of proteins.
</li>
<br>
<li style="font-size: 14px;">
<b>Sensitive</b>: This model provides a more sensitive prediction at the cost of longer computation time. This approach is useful in annotationg small number of proteins with high-quality prediction.
</li>
</ul>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-info" data-bs-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<div class="modal fade" id="errorModal" tabindex="-2" role="dialog" aria-labelledby="errorModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="mod-header modal-header">
<h5 class="modal-title" id="errorModalLabel">Error in Job Submission</h5>
<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close">
</button>
</div>
<div class="modal-body">
<p id="AtSubP2error">Error.</p>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-danger" data-bs-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
</div>
<div id="intermediate" class="container mt-5 d-none" >
<div class="row justify-content-center">
<code>
<div class="col-md-12">
<h4 class="my-2 text-center">Your query has been successfully submitted at LegumeLoc.</h4>
<br>
<h4 class="my-2 text-center">Please be patient while your query is being processed <img src="assets/images/test.gif" height="20"></h4>
<br>
<h4 class="my-2 text-center">After successfull completion of the job, you will be redirected to the results page:
</h4>
<br>
<br>
<h4 class ="text-center" id="AtSubP2SubmittionScreen">You have successfully submitted a query to LegumeLoc.</h4>
</div>
</code>
</div>
<div class='row mt-5 justify-content-center'>
<div class="col-md-2">
<a href="prediction.html" target="_blank" class="deepnec-btn-1 btn btn-primary" role="button">Submit another job</a>
</div>
</div>
</div>
<footer class="footer mt-5 mx-auto">
<div class="px-5">
<div class="line mt-2 mb-1"></div>
</div>
<div class="container d-flex flex-wrap py-1">
<p class="col-md-4 mb-0 text-copy" >© 2024 </p>
<a href="https://kaabil.net" target="_blank" class="d-flex align-items-center mx-2 mb-lg-0 me-lg-auto text-dark text-decoration-none">
<img src="./assets/images/lab_logo_red.png" style="height: 40px">
</a>
<a href="https://usu.edu" target="_blank" class="d-flex align-items-center mx-2 mb-lg-0 me-lg-auto text-dark text-decoration-none">
<img src="./assets/images/usu_logo3.png" style="height: 40px;">
</a>
</div>
</footer>
<script src="assets/js/prediction.js"></script>
</body>
</html>