-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathhelp.html
executable file
·219 lines (199 loc) · 12.4 KB
/
help.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
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>LegumeLoc - Help</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>
<style>
.container {
max-width: 1800px;
}
p {
text-indent: 40px;
}
</style>
</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" 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 active" href="help.html"><i
class="bi bi-question-square-fill mx-2"></i><span>User guide</span>
</a>
</div>
</div>
</div>
</nav>
</header>
<main class="flex-shrink-0">
<div class="container">
<h1 class="mt-4 mb-4 text-center">Help Page</h1>
<div class="row" style="margin-top: 5px;">
<div class="col-md-2"></div>
<div class="col-md-8" style="font-size: 18px;">
<div class="card m-b-20 card-body" style="text-align: justify;">
<div id="intro_loading" style="margin-bottom: 10px;"></div>
<h4><b class="text-muted2">Introduction</b></h4>
<p>
On this page, you will find a step-by-step guide to submit a query and obtain the result for protein localization
prediction. This page will also show the different options available for prediction and what each parameter means.
If you have any questions that are not covered on this page, please send an email to
<a href="mailto:[email protected]">[email protected]</a>.
</p>
<hr>
<h4><b class="text-muted2">Input Data</b></h4>
<p>
LegumeLoc server supports protein sequence(s) in FASTA format — you can either upload a FASTA file with protein
sequences, paste sequence(s) in the text area, or provide <a href="https://www.ncbi.nlm.nih.gov/">NCBI</a>/<a href="https://www.uniprot.org/">UniProt</a>
accession ID in the text box. A maximum of <b>10,000 sequences</b> can be analyzed on this server.
</p>
<img src='assets/images/input.png' width="750px" style="display: block; margin: 0 auto; border: 2px dotted rgb(165, 161, 161);">
<hr>
<h4><b class="text-muted2">Prediction Levels</b></h4>
<p>
LegumeLoc supports three levels for legume protien subcellular localization prediction. Users can select any level for
prediction and their preceeding levels will be automatically selected. For example, on selecting "Dual Localization
Classification" level, the levels before it will be automatically selected. By default, all the levels are selected,
which are explained below:
</p>
<p>
<u>Level I</u>: In this level, a query sequence is predicted as 'single' or 'dual' localization protein.
</p>
<p>
<u>Level II</u>: Selecting this level will first run <i>Level I</i>, followed by classifying the single localization proteins
into 11 single localization classes.
</p>
<p>
<u>Level III</u>: This level will first execute <i>Level I</i> and <i>Level II</i>, followed by classifying dual localization
proteins into 14 classes.
</p>
<p>
The available single or dual classes can be found in the information icon on the <a href="prediction.html">Prediction</a> page.
</p>
<img src='assets/images/prediction_options.png' width="800px" style="display: block; margin: 0 auto; border: 2px dotted rgb(141, 131, 131);">
<hr>
<h4><b class="text-muted2">Prediction Models</b></h4>
<p>
Two prediction strategies are available in LegumeLoc — <i>Fast</i> and <i>Sensitive</i> (as shown in the above figure).
On the <a href="prediction.html">Prediction</a> page, an information icon provides information about the models available.
</p>
<ol>
<li>
<b>Fast</b>: This model provides a faster prediction by using DPCP protein feature. This approach is useful for annotationg
a large number of proteins at once.
</li>
<li>
<b>Sensitive</b>: This model provides a more sensitive prediction at the cost of longer computation time. This approach
employs TPC protein feature and is useful for the annotation of small number of proteins with high-quality prediction.
</li>
</ol>
<hr>
<h4><b class="text-muted2">Localization Prediction</b></h4>
<p>
An (optional) email address can be provided to receive a link to the results when the analysis is completed. The
<i><b>Run Prediction</b></i> button will execute the prediction on LegumeLoc server. The link to the results (available
on query submission) can also be copied or bookmarked for later use.
</p>
<img src='assets/images/email_run.png' width="800px" style="display: block; margin: 0 auto; border: 2px dotted rgb(165, 161, 161);">
<hr>
<h4><b class="text-muted2">Output Example</b></h4>
<p>
The result table will change based on the prediction level selected. As shown below, results an be viewed for Level 1, Level 2,
or Level 3. The selected level will be red in color. For each level, the <i><b>Download Results</b></i> button can be used to
download the comprehensive results table in tab-delimited format.
</p>
<img src='assets/images/results.png' width="900px" style="display: block; margin: 0 auto; border: 2px dotted rgb(165, 161, 161);">
<hr>
<h4><b class="text-muted2">Browser Compatibility</b></h4>
<p>LegumeLoc has been tested in the following environments:</p>
<table class="table table-bordered">
<thead>
<tr>
<th>OS</th>
<th>Version</th>
<th>Chrome</th>
<th>Firefox</th>
<th>Safari</th>
<th>Edge</th>
</tr>
</thead>
<tbody>
<tr>
<td>Linux</td>
<td>Ubuntu 22.04</td>
<td>108.0.5359.71</td>
<td>112.0.2</td>
<td>n/a</td>
<td>113.0.1774.35</td>
</tr>
<tr>
<td>MacOS</td>
<td>Ventura 13.3.1 (a)</td>
<td>108.0.5359.71</td>
<td>112.0.2</td>
<td>16.4</td>
<td>113.0.1774.35</td>
</tr>
<tr>
<td>Windows</td>
<td>10</td>
<td>108.0.5359.71</td>
<td>112.0.2</td>
<td>not tested</td>
<td>113.0.1774.35</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</main>
<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>
</body>
</html>