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
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<link rel="stylesheet" type="text/css" href="logo.css">
<title>WebLogo 3 - User's Manual</title>
<meta http-equiv="Content-Type" content="text/html;charset=utf-8">
<meta name="author" content="Gavin E. Crooks">
<!-- Latest compiled and minified CSS -->
<link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
<!-- Optional theme -->
<link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap-theme.min.css">
<!-- Latest compiled and minified JavaScript -->
<script src="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
<!--CSS spacing adjustments for aligning definition lists under Bootstrap-->
<style type="text/css">
#create-sequence {
font-size: large
}
dd {
padding-top: 3px
}
#color-scheme {
padding-top: 2px
}
</style>
</head>
<body>
<div class="container-fluid">
<!--outermost container-->
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="./">WebLogo 3</a>
</div>
<div class="collapse navbar-collapse">
<ul class="nav navbar-nav">
<li><a href="./">home</a></li>
<li><a href="create.cgi">create</a></li>
<li><a href="examples.html">examples</a></li>
<li class="active"><a href="manual.html">manual</a></li>
</ul>
</div>
<!--/.nav-collapse -->
</div>
</div>
<!--close navbar container-->
<div class="container-fluid">
<!--outer fluid container-->
<div class="row">
<!--Manual.html text row container-->
<div class="col-sm-1"></div>
<!--outer left margin column-->
<div class="col-sm-10">
<!--central text column sm-10-->
<div class="row">
<!--table of contents container-->
<div class="row">
<h3><br></h3></div>
<!--spacing to push title below nav bar-->
<h1 id='Gallery-header'>WebLogo 3: User's Manual</h1>
<div>
<h4>Contents</h4></div>
<!--
<img alt="WebLogo: Create" width="499" height="633"
src="img/weblogo_create.png" align="right" border='1' vspace="10" hspace="10"></a>
-->
<div class="col-sm-6">
<!--table of contents left column: links-->
<ul>
<li><a href="#intro">Introduction</a></li>
<li><a href="#create">Creating Sequences Logos using the Web interface</a></li>
<li><a href="#download">Downloading and Installing WebLogo</a></li>
<li><a href="#CLI"> Command Line Interface (CLI)</a></li>
<li><a href="#API"> Application Programmer Interface (API)</a></li>
<li><a href="#dev"> Development and Future Features</a></li>
<li><a href="#misc">Miscellanea</a></li>
</ul>
</div>
<!--close table of contents left column: links-->
<div class="col-sm-6">
<!--table of contents right column: image-->
<img src="img/example.png" class="img-responsive" alt="Web Logo example">
</div>
<!--close table of contents right column: image-->
</div>
<!--table of contents container end-->
<div class="row">
<!--release notes row container-->
<h4> Release Notes and Known Bugs</h4> The <a href="weblogo_changelog.txt">WebLogo release notes</a> detail changes to WebLogo and known issues with particular versions.
</div>
<!--release notes container end-->
<div class="row">
<!--introductions container-->
<a name="intro">
<br>
</a>
<h2>Introduction</h2>
<p>
<strong>WebLogo</strong> is a web based application designed to make the
<a href="create.cgi">generation</a> of sequence logos as easy and painless as possible.
</p>
<p>
A <a href="https://alum.mit.edu/www/toms/sequencelogo.html">sequence logo</a> is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. The width of the stack is proportional to the fraction of valid symbols in that position. (Positions with many gaps have thin stacks.)In general, a sequence logo provides a richer and more precise description of, for example,a binding site, than would a consensus sequence.
</p>
</div>
<!--introductions container end-->
<!-- ============================================================== -->
<div class="row">
<!--references row container-->
<div>
<h4>References</h4></div>
<div>
<p>
<a href="http://threeplusone.com/">Crooks GE</a>,
<a href="http://compbio.berkeley.edu/">Hon G</a>,
<a href="http://compbio.berkeley.edu/">Chandonia JM</a>,
<a href="http://compbio.berkeley.edu/people/brenner/">Brenner SE</a> WebLogo: A sequence logo generator,
<em>Genome Research</em>, 14:1188-1190, (2004) [
<a href="http://threeplusone.com/pubs/fulltext/Crooks2004a-GR-WebLogo.pdf">Full Text</a> ]
</p>
<p>
Schneider TD, Stephens RM. 1990.
<a class="out" href="https://alum.mit.edu/www/toms/paper/logopaper/">Sequence Logos: A New Way to Display Consensus Sequences.</a>
<em>Nucleic Acids Res.</em> <em>18</em>:6097-6100
</p>
</div>
</div>
<!--end references row container-->
<!-- ============================================================== -->
<div class="row">
<!--creating Sequences Logos row container start-->
<div>
<a name="create">
<br>
</a>
<h2>Creating Sequences Logos using the Web interface</h2>
<dl class="dl-horizontal">
<!--start definition list Creating Sequences Logos using the Web interface -->
<dt id="create-sequence">Sequence Data</dt>
<dd>
Enter your multiple sequence alignment or position weight matrix file, or select a file to upload. Supported file formats include CLUSTALW, FASTA, plain flatfile, MSF, NBRF, PIR, NEXUS and PHYLIP for multiple sequence alignments, and transfac for position weight matrices. All sequences must be the same length, else WebLogo will return an error and report the first sequence that differed in length from previous sequences.
</dd>
<br>
<dt id="create-sequence">Output format</dt>
<dd>Generally speaking, vector formats (EPS and PDF) are better for print, while bitmaps (JPEG and PNG) are more suitable for displaying on the screen or embedding into a web page.
</dd>
<dd>
<table class="table table-bordered table-condensed">
<tr>
<td>PNG:</td>
<td>(600 DPI) Print resolution bitmap</td>
</tr>
<tr>
<td> PNG:</td>
<td>(low res, 96 DPI) Screen resolution bitmap </td>
</tr>
<tr>
<td>JPEG:</td>
<td> Screen resolution bitmap </td>
</tr>
<tr>
<td>EPS:</td>
<td> Encapsulated postscript </td>
</tr>
<tr>
<td>PDF:</td>
<td> Portable Document Format </td>
</tr>
<tr>
<td>SVG:</td>
<td> Scalable Vector Graphics </td>
</tr>
</table>
</dd>
<br>
<dt id="create-sequence">Logo size</dt>
<dd>The physical dimensions of the generated logo. Specifically, Logo Size controls the size of individual symbols stacks.
</dd>
<dd>
<table class="table table-bordered table-condensed">
<tr>
<td>small:</td>
<td> 5.4 points wide (same as 9pt Courier), aspect ratio 5:1 </td>
</tr>
<tr>
<td> medium:</td>
<td> Double the width and height of small.</td>
</tr>
<tr>
<td>large:</td>
<td> Triple the width and height of small. </td>
</tr>
</table>
<dd>
<small>The choices have been limited to promote inter-logo consistency. Small logos can fit 80 stacks across a printed page, or 40 across a half page column. The <a href="#CLI">command line interface</a> provides greater control, if so desired. </small>
</dd>
<br>
<dt id="create-sequence">Stacks per line</dt>
<dd>
If the length of the sequences is greater than this maximum number of stacks per line, then the logo will be split across multiple lines.
</dd>
<br>
<dt id="create-sequence">Sequence Type</dt>
<dd>Selects the type of biological molecule.
<table class="table table-bordered table-condensed">
<tr>
<td>auto: Automatically guess sequence type from the data</td>
</tr>
<tr>
<td>protein</td>
</tr>
<tr>
<td>dna</td>
</tr>
<tr>
<td>rna</td>
</tr>
</table>
</dd>
<br>
<dt style='white-space: normal' id="create-sequence">Ignore Lower Case</dt>
<dd>Disregard lower case letters and only count upper case letters in sequences</dd>
<br>
<dt id="create-sequence">Units</dt>
<dd>The units used for the y-axis. </dd>
<dd>
<table class="table table-bordered table-condensed">
<tr>
<td>probability:</td>
<td>Show residue probabilities, rather than information content. If <a href="#CA">compositional adjustment</a> is disabled, then these are the raw residue frequencies.</td>
</tr>
<tr>
<td>bits:</td>
<td> Information content in bits</td>
</tr>
<tr>
<td> nats:</td>
<td> Natural units, 1 bit = ln 2 (0.69) nats</td>
</tr>
<tr>
<td> kT:</td>
<td> Thermal energy units in natural units (numerically the same as nats) </td>
</tr>
<tr>
<td> kJ/mol:</td>
<td>Thermal energy (assuming T = 300 K) </td>
</tr>
<tr>
<td>kcal/mol:</td>
<td> Thermal energy (assuming T = 300 K) </td>
</tr>
</table>
</dd>
<a name="First position number">
<br>
</a>
<dt style='white-space: normal' id="create-sequence">First position number</dt>
<dd>
The numerical label of the first position in the sequence data in the input file. The label must be an integer. Residue labels for the logo will be relative to this number. (See also: <a href="#logo range">Logo range</a>.)
</dd>
<a name="logo range">
<br>
</a>
<dt id="create-sequence">Logo range</dt>
<dd>
By default, all sequence data from the input file is displayed in the Sequence Logo. With this option, you can instead show a subrange of the sequence data. The numbering of Start and End Positions is relative to the First Position Number. Thus, if the First Position Number is "2", Start is "5" and End is "10", then the 4th through 9th (inclusive) sequence positions of the input file will be displayed, and they will be numbered "5", "6", "7", "8", "9" and "10".
</dd>
<a name="CA">
<br>
</a>
<dt id="create-sequence">Composition</dt>
<dd>
<p>
The background composition of the genome or proteome from which the sequences have been drawn. The default, automatic option is to use equiprobable background for nucleic acids and a typical amino acid usage pattern for proteins. However, you may also explicitly set the expected CG content for nucleic acid sequences, insist on equiprobable background distributions, or turn off composition adjustment altogether.
</p>
<p>
Compositional adjustment has two effects. First, the information content of a site is defined as the relative entropy of the monomers at that site to the background distribution. Consequentially, rare monomers have higher information content (when they occur) than relatively common monomers.
</p>
<p>
Secondly, the background composition is used in the small sample correction of information content. Briefly, if only a few sequences are available in the multiple sequence alignment, then sites typically appear more conserved than they really are. Small samples bias the relative entropy upwards. To compensate, we add pseudocounts to the actual counts, proportional to the expected background composition. These pseudocounts smooth the data for small samples, but become irrelevant for large samples. The proportionality constant is set to 4 for nucleic acid sequences, and 20 for proteins (these numbers have been found to give reasonable results in practice).
</p>
<p>
Behind the scenes, things are more complex. We do a full Bayesian calculation, starting with explicit Dirichlet priors based on the background composition, to which we add the data and then calculate both the posterior mean relative entropy (the stack height) and Bayesian 95% confidence intervals for error bars. These interesting details will be explained elsewhere.
</p>
</dd>
<br>
<dt id="create-sequence">Scale stack width</dt>
<dd>
Scale the visible stack width by the fraction of symbols in the column.(I.e. columns with many gaps or unknown residues are narrow.)
</dd>
<br>
<dt id="create-sequence">Error bars</dt>
<dd>Display error bars. These indicate an approximate Bayesian 95% confidence interval.
</dd>
<br>
<dt id="create-sequence">Title</dt>
<dd>Give your logo a title.</dd>
<br>
<dt id="create-sequence">Figure label</dt>
<dd>An optional figure label, added to the top left (e.g. '(a)').</dd>
<br>
<dt id="create-sequence">X-axis</dt>
<dd>Add a label to the x-axis, or hide axis altogether.</dd>
<br>
<dt id="create-sequence">Y-axis</dt>
<dd>
The vertical axis indicates the information content of a sequence position. Use this option to toggle the y-axis and override the default axis label.
</dd>
<br>
<dt id="create-sequence">Y-axis scale</dt>
<dd>
The height of the y-axis in designated units. The automatic option will pick reasonable defaults based on the sequence type and axis unit.
</dd>
<br>
<dt id="create-sequence">Y-axis tic spacing</dt>
<dd>The distance between major tic marks on the y-axis.</dd>
<br>
<dt style='white-space: normal' id="create-sequence">Sequence end labels</dt>
<dd>
Choose this option to label the 5' & 3' ends of nucleic acid or the N & C termini of amino acid sequences.
</dd>
<br>
<dt id="create-sequence">Version fineprint</dt>
<dd>
Toggle display of the WebLogo version information in the lower right corner. Optional, but we appreciate the acknowledgment.
</dd>
<br>
</dl>
<!--end definition Creating Sequences Logos using the Web interface -->
<dt id="create-sequence">Color Scheme</dt>
<dl class="dl-horizontal">
<!--start definition list for Color Scheme section-->
<dt id="color-scheme"> Auto: </dt>
<dd> Use Base Pairing for nucleic acids (NA), Hydrophobicity for amino acids (AA). </dd>
<br>
<dt id="color-scheme"> Monochrome: </dt>
<dd>All symbols black </dd>
<br>
<dt style='white-space: normal'>Base Pairing
<br> (NA default):</dt>
<dd>
<table class="table table-bordered table-condensed">
<tr>
<td>2 Watson-Crick hydrogen bonds</td>
<td>TAU</td>
<td style="color:darkorange">dark orange</td>
</tr>
<tr>
<td>3 Watson-Crick hydrogen bonds</td>
<td>GC</td>
<td style="color:blue"> blue</td>
</tr>
</table>
</dd>
<p></p>
<dt> Classic (NA): </dt>
<dd>
<table class="table table-bordered table-condensed">
<tr>
<td>G</td>
<td style="color:orange"> orange</td>
</tr>
<tr>
<td>TU</td>
<td style="color:red"> red</td>
</tr>
<tr>
<td>C</td>
<td style="color:blue">blue</td>
</tr>
<tr>
<td>A</td>
<td style="color:green">green</td>
</tr>
</table>
<small>WebLogo (version 1 and 2) and makelogo default color scheme for nucleic acids: G, orange; T & U, red; C, blue; and A, green.</small>
</dd>
<br>
<dt style='white-space: normal'> Hydrophobicity
<br> (AA default): </dt>
<dd>
<table class="table table-bordered table-condensed">
<tr>
<td>Hydrophilic</td>
<td>RKDENQ</td>
<td style="color:blue">blue</td>
</tr>
<tr>
<td>Neutral</td>
<td>SGHTAP</td>
<td style="color:green"> green</td>
</tr>
<tr>
<td>Hydrophobic</td>
<td>YVMCLFIW</td>
<td style="color:black"> black</td>
</tr>
</table>
</dd>
<p></p>
<dt id="color-scheme"> Chemistry (AA): </dt>
<dd> Color amino acids according to chemical properties. </dd>
<dd>
<table class="table table-bordered table-condensed">
<tr>
<td>Polar</td>
<td>G,S,T,Y,C</td>
<td style="color:green"> green</td>
</tr>
<tr>
<td>Neutral</td>
<td>Q,N</td>
<td style="color:purple"> purple</td>
</tr>
<tr>
<td>Basic</td>
<td>K,R,H</td>
<td style="color:blue"> blue</td>
</tr>
<tr>
<td>Acidic</td>
<td>D,E</td>
<td style="color:red">red</td>
</tr>
<tr>
<td>Hydrophobic</td>
<td>A,V,L,I,P,W,F,M</td>
<td style="color:black">black</td>
</tr>
</table>
<small> WebLogo (version 1 and 2) and makelogo default color. (Note that the WebLogo 2 documentation erroneously lists Q and N under green.) </small>
</dd>
<br>
<dt id="color-scheme"> Charge (AA) : </dt>
<dd>
<table class="table table-bordered table-condensed">
<tr>
<td>Positive</td>
<td>KRH</td>
<td style="color:blue"> blue</td>
</tr>
<tr>
<td>Negative</td>
<td>DE</td>
<td style="color:red"> red</td>
</tr>
</table>
</dd>
<p></p>
<dt id="color-scheme"> Custom: </dt>
<dd>
A custom color scheme can be specified in the input field below. Specify colors on the left and associated symbols on the right. Colors are entered using <a href="http://www.w3.org/TR/REC-CSS2/syndata.html#color-units">CSS2 (Cascading Style Sheet)</a> syntax. (E.g. 'red', '#F00', '#FF0000', 'rgb(255, 0, 0)', 'rgb(100%, 0%, 0%)' or 'hsl(0, 100%, 50%)' for the color red.)
</dd>
<p>
<br>
</p>
</dl>
<!--End definition list for Color Scheme section-->
<dl class="dl-horizontal">
<dt id="create-sequence">More Options</dt>
<dd>
The weblogo <a href="#CLI">command line client</a>, <code class="code">weblogo</code>, provides many more options and greater control over the final logo appearance.
</dd>
</dl>
</div>
</div>
<!--Creating Sequences Logos row container end-->
<!-- ========================================================= -->
<div class="row">
<!--installing weblogo row container start-->
<a name="download">
<br>
</a>
<h2>Installing WebLogo</h2>
<dl>
<!-- start dinfinition list for Installing WebLogo-->
<dt>
<h4>Dependencies</h4></dt>
<dd>
WebLogo version 3 is written in python. It is necessary to have <a href="http://www.python.org/download/">Python 3.8 or later</a> and the extension package
<a href="http://www.scipy.org/Download">numpy</a> installed before WebLogo will run. WebLogo also requires a recent version of <a href="http://www.cs.wisc.edu/~ghost/">ghostscript</a> to create PNG and PDF output, and <a href="http://www.cityinthesky.co.uk/opensource/pdf2svg">pdf2svg</a> to generate SVG output.
</dd>
<dt>
<h4> Download and Installation</h4></dt>
<dd>
WebLogo and its dependencies can be downloaded and installed with pip,
<pre>
pip install weblogo
</pre>
or conda.
<pre>
conda install -c conda-forge weblogo
</pre>
Alternatively, weblogo and its dependencies can be installed manually. The WebLogo source code can be downloaded from
<a href="https://github.com/WebLogo/weblogo/issues">Weblogo's Github repository</a>. This code is distributed under various <a href="http://www.opensource.org/docs/definition">open source licenses</a>. Please consult the <code class="code">LICENSE.txt</code> file in the source distribution for details.
<p>
After unpacking the WebLogo tarfile, it should be possible to immediately create logos using the command line client (provided that python, numpy and ghostscript have already been installed).
</p>
<pre>
./weblogo --format PNG < cap.fa > cap.png
</pre>
<p>
Please consult the file <code class="code">build_examples.sh</code> for more examples. </p>
<p>
To run WebLogo as a stand alone web service, run the logo server command :
</p>
<pre>
./weblogo --serve
</pre>
<p>
It should now be possible to access WebLogo at <a href="http://localhost:8080/">http://localhost:8080/</a>.
</p>
</dd>
<dt>
<h4>Web App</h4></dt>
<dd>
To use WebLogo as a web application, first install the weblogo dependencies and libraries as above, then place (or link) the
<code class="code">weblogo/htdocs</code> directory somewhere within the document root of your webserver. The webserver must be able to execute the CGI script <code class="code">create.cgi</code>. For Apache, you may have to add an <code class="code">ExecCGI</code> option and add a cgi handler in the <code class="code">httpd.conf</code> configuration file. Something like this:
<pre>
DocumentRoot "/home/ec2-user/weblogo/weblogo/htdocs"
# Further relax access to the default document root:
<Directory "/home/ec2-user/weblogo/weblogo/htdocs">
Options Indexes FollowSymLinks ExecCGI MultiViews
AddHandler cgi-script .cgi
AllowOverride All
Require all granted
</Directory>
</pre> It may also be necessary to set the <code class="code">PATH</code> and <code class="code">PYTHONPATH</code> environment variables.
<pre>
SetEnv PYTHONPATH /path/to/weblogo/libraries
</pre> The cgi script also has to be able to find the '<code class="code">gs</code>' ghostscript executable.
</pre> The maximum bytes of uploaded sequence data can be controlled with the <code class="code">WEBLOGO_MAX_FILE_SIZE</code> environment variable.
<pre>
SetEnv WEBLOGO_MAX_FILE_SIZE 1000000
</pre>
</dd>
</dl>
<!--end definition list for Installing Weblogo-->
</div>
<!--installing Weblogo row container close-->
<!-- ================================================================== -->
<div class="row">
<!--WebLogo Command Line Interface row container start-->
<a name="CLI">
<br>
</a>
<dl>
<!--start definition list for Weblogo CLI-->
<dt>
<h2><code class="code">weblogo</code>, The WebLogo Command Line Interface (CLI)</h2></dt>
<dd>
The command line client has many options not available through the web interface. Please consult the bundled <code class="code">build_examples.sh</code> script for inspiration.
<pre>
Usage: weblogo [options] < sequence_data.fa > sequence_logo.eps
Create sequence logos from biological sequence alignments.
Options:
--version show program's version number and exit
-h --help show this help message and exit
Input/Output Options:
-f --fin FILENAME Sequence input file (default: stdin)
--upload URL Upload input file from URL
-D --datatype FORMAT Type of multiple sequence alignment or
position weight matrix file: (clustal, fasta,
msf, genbank, nbrf, nexus, phylip, stockholm,
intelligenetics, table, array, transfac)
-o --fout FILENAME Output file (default: stdout)
-F --format FORMAT Format of output: eps (default), png,
png_print, pdf, jpeg, svg, logodata
Logo Data Options:
-A --sequence-type TYPE The type of sequence data: 'protein', 'rna' or
'dna'.
-a --alphabet ALPHABET The set of symbols to count, e.g. 'AGTC'. All
characters not in the alphabet are ignored. If
neither the alphabet nor sequence-type are
specified then weblogo will examine the input
data and make an educated guess. See also
--sequence-type, --ignore-lower-case
-U --units UNIT A unit of entropy ('bits' (default), 'nats',
'digits'), or a unit of free energy ('kT',
'kJ/mol', 'kcal/mol'), or 'probability' for
probabilities
--composition COMP. The expected composition of the sequences:
'auto' (default), 'equiprobable', 'none' (do
not perform any compositional adjustment), a
CG percentage, a species name (e.g. 'E. coli',
'H. sapiens'), or an explicit distribution
(e.g. "{'A':10, 'C':40, 'G':40, 'T':10}"). The
automatic option uses a typical distribution
for proteins and equiprobable distribution for
everything else.
--weight NUMBER The weight of prior data. Default depends on
alphabet length
-i --first-index INDEX Index of first position in sequence data
(default: 1)
-l --lower INDEX Lower bound of sequence to display
-u --upper INDEX Upper bound of sequence to display
Transformations:
Optional transformations of the sequence data.
--ignore-lower-case Disregard lower case letters and only count
upper case letters in sequences.
--reverse reverse sequences
--complement complement nucleic sequences
--revcomp reverse complement nucleic sequences
Logo Format Options:
These options control the format and display of the logo.
-s --size LOGOSIZE Specify a standard logo size (small, medium
(default), large)
-n --stacks-per-line COUNT Maximum number of logo stacks per logo line.
(default: 40)
-t --title TEXT Logo title text.
--label TEXT A figure label, e.g. '2a'
-X --show-xaxis YES/NO Display sequence numbers along x-axis?
(default: True)
-x --xlabel TEXT X-axis label
--annotate TEXT A comma separated list of custom stack
annotations, e.g. '1,3,4,5,6,7'. Annotation
list must be same length as sequences.
--rotate-numbers YES/NO Draw X-axis numbers with vertical orientation
(default: False).
--number-interval NUMBER
Distance between numbers on X-axis (default:
5)
-S --yaxis NUMBER Height of yaxis in units. (Default: Maximum
value with uninformative prior.)
-Y --show-yaxis YES/NO Display entropy scale along y-axis? (default:
True)
-y --ylabel TEXT Y-axis label (default depends on plot type and
units)
-E --show-ends YES/NO Label the ends of the sequence? (default:
False)
-P --fineprint TEXT The fine print (default: weblogo version)
--ticmarks NUMBER Distance between ticmarks (default: 1.0)
--errorbars YES/NO Display error bars? (default: True)
--reverse-stacks YES/NO Draw stacks with largest letters on top?
(default: True)
Color Options:
Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc.
-c --color-scheme SCHEME Specify a standard color scheme (auto, base
pairing, charge, chemistry, classic,
hydrophobicity, monochrome)
-C --color COLOR SYMBOLS DESCRIPTION
Specify symbol colors, e.g. --color black AG
'Purine' --color red TC 'Pyrimidine'
--default-color COLOR Symbol color if not otherwise specified.
Font Format Options:
These options provide control over the font sizes and types.
--fontsize POINTS Regular text font size in points (default: 10)
--title-fontsize POINTS Title text font size in points (default: 12)
--small-fontsize POINTS Small text font size in points (default: 6)
--number-fontsize POINTS
Axis numbers font size in points (default: 8)
--text-font FONT Specify font for labels (default: ArialMT)
--logo-font FONT Specify font for logo (default: Arial-BoldMT)
--title-font FONT Specify font for title (default: ArialMT)
Advanced Format Options:
These options provide fine control over the display of the logo.
-W --stack-width POINTS Width of a logo stack (default: 10.8)
--aspect-ratio POINTS Ratio of stack height to width (default: 5)
--box YES/NO Draw boxes around symbols? (default: no)
--resolution DPI Bitmap resolution in dots per inch (DPI).
(Default: 96 DPI, except png_print, 600 DPI)
Low resolution bitmaps (DPI<300) are
antialiased.
--scale-width YES/NO Scale the visible stack width by the fraction
of symbols in the column? (I.e. columns with
many gaps of unknowns are narrow.) (Default:
yes)
--debug YES/NO Output additional diagnostic information.
(Default: False)
--errorbar-fraction NUMBER
Sets error bars display proportion (default:
0.9)
--errorbar-width-fraction NUMBER
Sets error bars width display proportion
(default: 0.25)
--errorbar-gray NUMBER Sets error bars' gray scale percentage
(default: 0.75)
WebLogo Server:
Run a standalone webserver on a local port.
--serve Start a standalone WebLogo server for creating
sequence logos.
--port PORT Listen to this local port. (Default: 8080)
</pre>
</dd>
</dl>
<!--end definition list for Weblogo CLI-->
</div>
<!--WebLogo Command Line Interface row container end-->
<!-- ===================================================================== -->
<div class="row">
<!--Weblogo API row container start -->
<a name="API" ><br></a>
<h2>WebLogo Application Programmer Interface (API)</h2>
The WebLogo python libraries provide even greater flexibility than the command line client.
Please consult the code documentation at <a href="https://weblogo.readthedocs.io/en/latest/">readthedocs</a>.
</div><!--Weblogo API row container end-->
<!-- ================================================================== -->
<div class="row">
<!--start WebLogo Development row Container-->
<a name="dev">
<br>
</a>
<h2>WebLogo Development and Future Features</h2>
<p>
The development project is hosted at
<a href="https://github.com/WebLogo/weblogo">https://github.com/WebLogo/weblogo</a>. If you wish to extend WebLogo or to contribute code, then you should download the full source code development package directly from the Github repository.
</p>
<pre>
> git clone https://github.com/WebLogo/weblogo
> pip install -e .
> cd weblogo
</pre>
<p>
Please consult the developer notes, <code class="code">DEVELOPERS.txt</code> and software license <code class="code">LICENSE.txt</code>
</p>
<p>
Outstanding bugs and feature requests are listed on the <a href="https://github.com/WebLogo/weblogo/issues">WebLogo issue tracker.</a>
</p>
</div>
<!--end WebLogo Development row Container-->
<!-- ================================================================== -->
<div class="row">
<!--Miscellanea row Container start-->
<a name="misc">
<br>
</a>
<h2>Miscellanea</h2>
<dl>
<!--start defined list Miscellanea-->
<dt>
<h4>WebLogo 2</h4></dt>
<dd> The legacy WebLogo 2 sever can be found <a href="http://weblogo.berkeley.edu/">here.</a>
</dd>
<dt>
<h4>Acknowledgments</h4></dt>
<dd>
<p>
WebLogo was created by
<a href="http://threeplusone.com/">Gavin E. Crooks</a>,
<a href="http://compbio.berkeley.edu/">Liana Lareau</a>,
<a href="http://compbio.berkeley.edu/">Gary Hon</a>,
<a href="http://compbio.berkeley.edu/">John-Marc Chandonia</a> and
<a href="http://compbio.berkeley.edu/people/brenner/">Steven E. Brenner</a>.
<a href="weblogo_changelog.txt">Many others</a> have provided suggestions, bug fixes and moral support.
</p>
</dd>
<dd>
<p>
WebLogo was originally based upon the programs
<a href="https://alum.mit.edu/www/toms/delila/alpro.html">alpro</a> and
<a href="https://alum.mit.edu/www/toms/delila/makelogo.html">makelogo</a>, both of which are part of Tom Schneider's
<a href="https://alum.mit.edu/www/toms/delila.html">delila</a> package. Many thanks are due to him for making this software freely available and for encouraging its use.
</p>
</dd>
<dt>
<h4>Disclaimer</h4></dt>
<dd>
<p>
While no permanent records are kept of submitted sequences, we cannot undertake to guarantee that data sent to WebLogo remains secure. Moreover, no guarantees whatsoever are provided about data generated by WebLogo.
</p>
</dd>
<dt>
<h4>Feedback</h4></dt>
<dd>
<p>
Suggestions on how to improve WebLogo are heartily welcomed! Please direct questions to <a href="https://github.com/WebLogo/weblogo/issues"> WebLogo's issue tracker</a>.
</p>
</dd>
</dl>
<!--end defined list Miscellanea-->
</div>
<!--Miscellanea Container row end-->
<!-- ================================================================== -->
<div class="row" id="spacing-row">
<hr>
</div>
<!--offset for bottom margin-->
</div>
<!--end central text col-sm-10-->
<div class="col-sm-1"></div>
<!--spacing right margin column-->
</div>
<!--Manual.html text Row Container End -->
</div>
<!--end outer container fluid-->
</div>
<!--OutermostContainer end-->
<!--fallback to server-hosted files in case CDNs fail-->
<!--google analytics-->
<script type="text/javascript">
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
</script>
<script type="text/javascript">
var pageTracker = _gat._getTracker("UA-5951066-1");
pageTracker._trackPageview();
</script>
</body>
</html>
|
