-
Notifications
You must be signed in to change notification settings - Fork 0
/
ampdb-tutorial.php
402 lines (397 loc) · 23.1 KB
/
ampdb-tutorial.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
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
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="shortcut icon" href="logo.png" type="image/x-icon">
<title>AMPDB Tutorial</title>
<link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.1.3/css/bootstrap.min.css" rel="stylesheet" />
<link href="https://cdn.datatables.net/1.13.3/css/dataTables.bootstrap5.min.css" rel="stylesheet" />
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.4/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.1.3/js/bootstrap.bundle.min.js"></script>
<script src="https://cdn.datatables.net/1.13.3/js/jquery.dataTables.min.js"></script>
<script src="https://cdn.datatables.net/1.13.3/js/dataTables.bootstrap5.min.js"></script>
</head>
<body>
<nav class="navbar navbar-expand-sm navbar-dark bg-dark fixed-top">
<div class="container-fluid">
<a class="navbar-brand fs-3" href="ampdb-home">AMPDB v1</a>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#mynavbar">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="mynavbar">
<ul class="navbar-nav me-auto">
<li class="nav-item">
<a class="nav-link" href="ampdb-home">Home</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown">Search</a>
<ul class="dropdown-menu">
<li><a class="dropdown-item" href="ampdb-text-search">Text Search</a></li>
<li><a class="dropdown-item" href="ampdb-specific-search">Specific Text Search</a></li>
<li><a class="dropdown-item" href="ampdb-target-organism-search">Search by Target
Organism</a></li>
<li><a class="dropdown-item" href="ampdb-pp-search">Search by Physicochemical Properties</a>
</li>
<li><a class="dropdown-item" href="ampdb-composition-search">Search by Protein
Composition</a>
</li>
<li><a class="dropdown-item" href="ampdb-activity-search">Search by Activity</a></li>
<li><a class="dropdown-item" href="ampdb-advanced-search">Advanced Search</a></li>
</ul>
</li>
<li class="nav-item">
<a class="nav-link" href="browse-all-data">Browse</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-classification">Classification</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown">Tools</a>
<ul class="dropdown-menu">
<li><a class="dropdown-item" href="https://ampdb-protein-sequence-alignment-toolbox.streamlit.app/" target="_blank">Protein Sequence Alignment Toolbox</a></li>
<li><a class="dropdown-item" href="https://ampdb-protein-feature-calculation-toolbox.streamlit.app/" target="_blank">Protein Feature Calculation Toolbox</a></li>
</ul>
<li class="nav-item">
<a class="nav-link" href="ampdb-data-stat">Statistics</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-downloads">Downloads</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-news">News/Updates</a>
</li>
<li class="nav-item">
<a class="nav-link" href="developers">Developers</a>
</li>
<li class="nav-item">
<a class="nav-link active" href="ampdb-tutorial">Tutorial</a>
</li>
<li class="nav-item">
<a class="nav-link" href="contact">Contact</a>
</li>
</ul>
<form class="d-flex" action="ampdb-quick-search-result" method="get">
<input name="term" class="form-control me-2" type="text" placeholder="Quick Search">
<input type="submit" value="Search" name="search" class="btn btn-primary">
</form>
</div>
</div>
</nav>
<br><br><br>
<div class="container">
<div class="row">
<div class="col-sm text-center" style="margin-top: 2%;">
<h4 style="font-weight: 500; color: #9A3863;">AMPDB Tutorial</h4>
</div>
</div>
</div>
<div class="container-fluid border border-4 mt-4 pt-2 pb-2" style="width: 85%;">
<div class="row">
<div class="col-sm">
<div style="text-align: left;">
<div style="text-align: left;"><b style="font-weight: 500; font-size: larger;">1. Use AMPDB Quick
Search
Facility</b></div>
<div style="text-align: justify;">
This is also a generelized search facility like text search. This
search facility is case insensitive. A user can search any search term (shown in example of SelBioDB Text Search). No search restriction is allowed here.
</div>
</div>
</div>
</div>
</div>
<div class="container-fluid border border-4 mt-4 pt-2 pb-2" style="width: 85%;">
<div class="row">
<div class="col-sm">
<div style="text-align: left;"><b style="font-weight: 500; font-size: larger;">2. Use AMPDB Text Search
Facility</b></div>
<div style="text-align: justify;">This is a generelized search facility (the
search can also be restricted by clicking on 'Choose
a Dataset' option). This
search facility is case insensitive.
Here one can search with followings.
</div>
<div class="text-start" style="font-size: small;">1. AMPDB ID (e.g., AMPDB_101)
</div>
<div class="text-start" style="font-size: small;">2. AMP from a Organism (e.g.,
Papio anubis)</div>
<div class="text-start" style="font-size: small;">3. AMP name (e.g., Defensin)
</div>
<div class="text-start" style="font-size: small;">4. Gene name of any AMP (e.g.,
LBP)</div>
<div class="text-start" style="font-size: small;">5. AMP Sequence (e.g.,
'MKLSTSLLAIVAVA') <br><span style="font-size: smaller; color: #121259; font-weight: 500;"><i>Note:
This is not BLAST search</i></span></div>
<div class="text-start" style="font-size: small;">6. Existence level of a
protein (e.g., Inferred from homology)</div>
<div class="text-start" style="font-size: small;">7. Target-organism (e.g.,
E.coli) <br><span style="font-size: smaller; color: #121259; font-weight: 500;"><i>Note:
For more specific target-organism search "Search by Target Organism"
search facility is recomended.</i></span></div>
<div class="text-start" style="font-size: small;">8. Antimicrobial activity of
an AMP (e.g., Fungicide)</div>
<div class="text-start" style="font-size: small;">9. Enzymatic activity of an
AMP (e.g., Protease)</div>
<div class="text-start" style="font-size: small;">10. Inhibitory activity of an
AMP (e.g., Protease inhibitor)</div>
<div class="text-start" style="font-size: small;">11. Other biological activity
(e.g., Cytokine) <br><span style="font-size: smaller; color: #121259; font-weight: 500;"><i>Note:
For perform more specific 8 to 11 related search "Search by
Activity" search facility is recomended.</i></span></div>
<div class="text-start" style="font-size: small;">12. PubMed ID (e.g., 25342741)
</div>
<div class="text-start" style="font-size: small;">13. PDB ID (e.g., 2MN5)</div>
<div class="text-start" style="font-size: small;">14. IntAct ID (e.g., O16829)
</div>
<div class="text-start" style="font-size: small;">15. STRING ID (e.g.,
9606.ENSP00000249330)</div>
<div class="text-start" style="font-size: small;">16. MINT ID (e.g., O60814)
</div>
<div class="text-start" style="font-size: small;">17. DIP ID (e.g., DIP-26293N)
</div>
<div class="text-start" style="font-size: small;">18. BioGRID ID (e.g., 124439)
</div>
<div class="text-start" style="font-size: small;">19. BindingDB ID (e.g.,
P00697)</div>
<div class="text-start" style="font-size: small;">20. ChEMBL ID (e.g.,
CHEMBL2297)</div>
<div class="text-start" style="font-size: small;">21. DrugBank ID(e.g., DB06934)
</div>
<div class="text-start" style="font-size: small;">22. GeneID (e.g., 1258585)
</div>
<div class="text-start" style="font-size: small;">23. KEGG ID (e.g., vg:1258585)
</div>
<div class="text-start" style="font-size: small;">24. Ensembl (e.g.,
ENSMGAT00000011853)</div>
<div class="text-start" style="font-size: small;">25. GeneTree ID (e.g.,
ENSGT00940000153832)</div>
<div class="text-start" style="font-size: small;">26. BRENDA ID (e.g., 3.2.1.17)
</div>
<div class="text-start" style="font-size: small;">27. BioCyc ID (e.g.,
ARA:AT3G12500-MON)</div>
<div class="text-start" style="font-size: small;">28. RNAct ID (e.g., P20160)
</div>
<div class="text-start" style="font-size: small;">29. PANTHER ID (e.g.,
PTHR10206)</div>
<div class="text-start" style="font-size: small;">30. PROSITE ID (e.g., PS00946)
</div>
<div class="text-start" style="font-size: small;">31. InterPro ID (e.g.,
IPR018216)</div>
<div class="text-start" style="font-size: small;">32. EMBL ID (e.g., Y09471)
</div>
<div class="text-start" style="font-size: small;">33. GenBank ID (e.g.,
BC142014)</div>
<div class="text-start" style="font-size: small;">34. CCDS ID (e.g.,
CCDS12044.1)</div>
<div class="text-start" style="font-size: small;">35. RefSeq ID (e.g.,
NP_001691.1)</div>
<div class="text-start" style="font-size: small;">36. UniProt ID (e.g., P19171)
<br><span style="font-size: smaller; color: #121259; font-weight: 500;"><i>Note:
For perform more specific 12 to 36 related search "Advanced Search"
facility is recomended.</i></span>
</div>
<div class="text-start" style="font-size: small;">37. Taxonomy lineage (e.g., Plant)</div>
<div class="text-start" style="font-size: small; display: none;"> (e.g., )</div>
</div>
</div>
</div>
<div class="container-fluid border border-4 mt-4 pt-2 pb-2" style="width: 85%;">
<div class="row">
<div class="col-sm">
<div style="text-align: left;"><b style="font-weight: 500; font-size: larger;">3. AMPDB Specific Search
Facility</b></div>
<div style="text-align: justify;">This is a specific search facility (the
search can also be restricted by clicking on 'Choose
a Dataset' option). This
search facility returns those entries which are exactly match with the
search term. This search facility is case insensitive.
Here one can search with followings.
</div>
<div>All the same search terms like the "AMPDB Text Search Facility" can also be search here</div>
</div>
</div>
</div>
<div class="container-fluid border border-4 mt-4 pt-2 pb-2" style="width: 85%;">
<div class="row">
<div class="col-sm">
<div style="text-align: left;"><b style="font-weight: 500; font-size: larger;">4. Use AMPDB Target
Organism
Search
Facility</b></div>
<div style="text-align: justify;">This search facility specifically designed
to
find one or more target organism of a AMP (the
search can also be restricted by clicking on 'Choose
a Dataset' option).
This search facility is case insensitive.
Here one can search in the following way.
</div>
<div class="text-start mt-3">
<span style="font-weight: 500;"> By single target organism name </span>
<hr style="margin-top: 0.5%; margin-bottom: 0.3%;">
<div style="padding-left: 1%; padding-right: 3%;">
Just type the organism name in the search box (e.g., E.coli or
e.coli).
</div>
</div>
<div class="text-start mt-3">
<span style="font-weight: 500;"> By Multiple target organism name (comma
separated or comma space separated) </span>
<hr style="margin-top: 0.5%; margin-bottom: 0.3%;">
<div style="padding-left: 1%; text-align: justify; padding-right: 3%;">
Type multiple organism name in the search box separated by comma or
comma space
(e.g., E.coli,S.typhimurium or e.coli, S.typhimurium). One can place
as
many organism as possible.
But this facility will return only those result which contain both
target organism.
</div>
</div>
<div class="mt-3" style="font-size: smaller; text-align: justify; padding-left: 1%; padding-right: 3%;">
<i>Note: In some case user may not find the target organism. In that
case we
suggest to do not
write anything on the search box, just click on "Get Organism from
Table" option. A table will
apprear. The table contain all target organism that we enlisted. You
need to find wheather
your target organism is enlisted in the table or not. You can search
in
different way (e.g.,
Escherichia coli can also write as it is or Escherichia sp. or
Escherichia spp.
or Escherichia species or E.coli or Escherichia). If your target
organism is enlisted in this table then
you nedd to write the same way in the "AMPDB Target Organism Search"
facility to find the result.
Do not bother about case sensitivity.</i>
</div>
</div>
</div>
</div>
<div class="container-fluid border border-4 mt-4 pt-2 pb-2" style="width: 85%;">
<div class="row">
<div class="col-sm">
<div style="text-align: left;"><b style="font-weight: 500; font-size: larger;">5. Use AMPDB
Protein Physicochemical Properties Search Facility</b></div>
<div style="text-align: justify;">This is protein physicochemical properties search
facility (the
search can also be restricted by clicking on 'Choose
a Dataset' option). Here
One can search by build query by just select the options(s) as need. The user need to click on the "Add Field" to make all fields and options visible.
</div>
<div class="text-start" style="font-size: small;">
In all the search field integer of float value expected.
A field may be kept blank to build the query.
A sample query is atached below in iamge form.
</div>
<div class="container">
<div class="row mt-2">
<div class="col-sm text-center">
<img src="ppquerybuild.png" alt="" srcset="" height="auto" width="98%">
</div>
</div>
</div>
</div>
</div>
</div>
<div class="container-fluid border border-4 mt-4 pt-2 pb-2" style="width: 85%;">
<div class="row">
<div class="col-sm">
<div style="text-align: left;"><b style="font-weight: 500; font-size: larger;">6. Use AMPDB
Protein Composition Search Facility</b></div>
<div style="text-align: justify;">This is Protein Composition search facility (the
search can also be restricted by clicking on 'Choose
a Dataset' option). Here
One can search by build query by just select the options(s) as need.The user need to click on the "Add Field" to make all fields and options visible.
</div>
<div class="text-start" style="font-size: small;">
In all the search field integer of float value expected.
A field may be kept blank to build the query.
A sample query is atached below in iamge form.
</div>
<div class="container">
<div class="row mt-2">
<div class="col-sm text-center">
<img src="pcquerybuild.png" alt="" srcset="" height="auto" width="98%">
</div>
</div>
</div>
</div>
</div>
</div>
<div class="container-fluid border border-4 mt-4 pt-2 pb-2" style="width: 85%;">
<div class="row">
<div class="col-sm">
<div style="text-align: left;"><b style="font-weight: 500; font-size: larger;">7. Use AMPDB
Activity Search Facility</b></div>
<div style="text-align: justify;">
In this section various activities are listed, which are
found in a AMP. A user can
select single or multiple checkbox(s) as per interest. The
search can also be restricted by clicking on 'Choose
a Dataset' option.
</div>
</div>
</div>
</div>
<div class="container-fluid border border-4 mt-4 pt-2 pb-2" style="width: 85%;">
<div class="row">
<div class="col-sm">
<div style="text-align: left;"><b style="font-weight: 500; font-size: larger;">8. Use AMPDB
Advanced Search
Facility</b></div>
<div style="text-align: justify;">
This is the most advanced search facility of AMPDB, where a user can build the query as he/she wants and search on the database. The search can also be restricted by clicking on 'Choose a Dataset' option. We recommend users to check the demo on advanced search facility of AMPDB on tutorial page.
A tutorial demo will add here soon.
</div>
</div>
</div>
</div>
<div class="container-fluid border border-4 mt-4 pt-2 pb-2" style="width: 85%;">
<div class="row">
<div class="col-sm">
<div style="text-align: left;"><b style="font-weight: 500; font-size: larger;">9. Understand the Text Format of AMPDB</b></div>
<div>The text format of AMPDB starts with two-character code followed by 4 blank space characters followed by the data. Each line is kept 80 characters long for better readability of the data. The description of the two-character code is given below.</div>
<div class="table-responsive border border-3 mt-2">
<table class="table table-striped table-hover">
<thead>
<tr>
<th style="font-weight: 500;">2 Character Code</th>
<th style="font-weight: 500;">Description</th>
</tr>
</thead>
<tbody>
<?php
require 'dbcon.php';
$sql = "SELECT * FROM txt_fmt";
$result = $con->query($sql);
while ($row = $result->fetch_assoc()) {
?>
<tr>
<td><?= $row['twoChar']; ?></td>
<td><?= $row['det']; ?></td>
</tr>
<?php
}
$con->close();
?>
</tbody>
</table>
</div>
</div>
</div>
</div>
<br><br><br>
<div class="container-fluid fixed-bottom">
<div class="row">
<div class="col-sm text-center text-white p-1" style="font-size: small; background-color: #5A6F80;">
© 2023 B&BL, DoAS, IIIT-A, UP-211015, India
</div>
</div>
</div>
</body>
</html>