Mercurial > repos > davidmurphy > codonlogo

comparison weblogolib/htdocs/manual.html @ 4:4d47ab2b7bcc

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidmurphy
date Fri, 13 Jan 2012 07:18:19 -0500
parents c55bdc2fb9fa
children
comparison
equal deleted inserted replaced
3:09d2dac9ef73 4:4d47ab2b7bcc
1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
2 "http://www.w3.org/TR/html4/transitional.dtd">
3 <html>
4 <head>
5 <link rel="stylesheet" type="text/css" href="logo.css" >
6 <title>CodonLogo - User's Manual</title>
7 <meta name="author" content="Gavin E. Crooks" >
8
9 <style type="text/css">
10 </style>
11 </head>
12
13 <body style="align:center">
14
15 <table width="80%" border = '0' cellspacing='0' cellpadding='1' align="center">
16 <tr><td >
17 <h1>CodonLogo 1.0: User's Manual</h1>
18
19 </td><td align = "right" >
20 &middot;
21 <a href="./">about</a>&nbsp;&middot;
22 <a href="create.cgi">create</a>&nbsp;&middot;
23 <a href="examples.html">examples</a>&nbsp;&middot;
24 <a class="selected" href="manual.html">manual</a>&nbsp;&middot;
25 <br>
26 <span style="font-size:small">&nbsp;</span>&nbsp;&nbsp;
27
28 </td></tr>
29
30 <tr><td colspan="2" class="discourse">
31
32 <h4>Contents</h4>
33
34 <img alt="Sequence logo example."
35 src="img/example.png" align="right" vspace="5" hspace="10">
36 <!--
37 <img alt="WebLogo: Create" width="499" height="633"
38 src="img/weblogo_create.png" align="right" border='1' vspace="10" hspace="10"></a>
39 -->
40
41 <ul>
42 <li><a href="#intro">Introduction</a>
43 </li><li><a href="#create">Creating Sequences Logos using the Web interface</a>
44 </li><li><a href="#download">Downloading and Installing CodonLogo</a>
45 </li><li><a href="#CLI"> Command Line Interface (CLI)</a>
46 </li><li><a href="#API"> Application Programmer Interface (API)</a>
47 </li><li><a href="#dev"> Development and Future Features</a>
48 </li><li><a href="#misc">Miscellanea</a>
49 </li>
50 </ul>
51
52
53 <a name="intro" ></a><h2>Introduction</h2>
54
55
56 <p>
57 <strong>CodonLogo</strong>
58 is a web based application designed to make the
59 <a href="create.cgi">generation</a> of
60 codon sequence logos as easy and painless as possible.
61 It is almost entirely based on the application WebLogo.
62 </p>
63
64
65 <p>
66 <a href="http://www.lecb.ncifcrf.gov/~toms/sequencelogo.html">Sequence&nbsp;logos</a>
67 are a graphical representation of an amino acid
68 or nucleic acid multiple sequence alignment.
69 Each logo consists of stacks of symbols, one stack for each position in the
70 sequence. The overall height of the stack indicates the sequence conservation
71 at that position, while the height of symbols within the stack indicates the
72 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 gasp have thin stacks.) In general, a sequence logo provides a richer and more precise description of, for example,
73 a binding site, than would a consensus sequence.
74 </p>
75
76
77
78
79
80
81
82 <!-- ============================================================== -->
83
84 <h4>References</h4>
85
86
87 <p>
88 <a href="http://bespoke.lbl.gov/">Crooks GE</a>,
89 <a href="http://compbio.berkeley.edu/">Hon G</a>,
90 <a href="http://compbio.berkeley.edu/">Chandonia JM</a>,
91 <a href="http://compbio.berkeley.edu/people/brenner/">Brenner SE</a>
92 WebLogo: A sequence logo
93 generator,
94 <em>Genome Research</em>, 14:1188-1190, (2004)
95 [<a href="http://bespoke.lbl.gov/pubs/fulltext/Crooks2004a-GR-WebLogo.pdf">Full Text</a> ]
96 </p>
97
98 <p>
99 Schneider TD, Stephens RM. 1990.
100 <a class="out" href="http://www.lecb.ncifcrf.gov/~toms/paper/logopaper/">Sequence Logos: A New Way to Display Consensus Sequences.</a>
101 <em>Nucleic Acids Res.</em> <em>18</em>:6097-6100
102 </p>
103
104
105
106
107
108
109
110 <a name="create" ></a>
111 <h2>Creating Sequences Logos using the Web interface</h2>
112
113
114 <h4>Sequence Data</h4>
115 Enter your multiple sequence alignment here, or select a file to upload. Supported file formats include CLUSTALW, FASTA, plain flatfile, MSF, NBRF, PIR, NEXUS and PHYLIP. All sequences must be the same length, else CodonLogo will return an error and report the first sequence that differed in length from previous sequences.
116
117 <h4>Output format</h4>
118
119 <ul>
120 <li> PNG : (600 DPI) Print resolution bitmap
121 </li><li> PNG : (low res, 96 DPI) Screen resolution bitmap
122 </li><li> JPEG :Screen resolution bitmap
123 </li><li> EPS : Encapsulated postscript
124 </li><li> PDF : Portable Document Format
125 </li>
126 </ul>
127 Generally speaking, vector formats (EPS and PDF) are better for printing, while bitmaps (JPEG and PNG) are more suitable for displaying on the screen or embedding into a web page.
128
129 <h4>Logo size</h4>
130 The physical dimensions of the generated logo.
131 Specifically, controls the size of individual symbols stacks.
132 <ul>
133 <li> small : 5.4 points wide (Same as 9pt Courier), aspect ratio 5:1
134 </li><li> medium : Double the width and height of small.
135 </li><li> large : Triple the width and height of small.
136 </li>
137 </ul>
138 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.
139
140 <h4>Stacks per line</h4>
141 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.
142
143 <h4>Sequence type</h4>
144 The type of biological molecule.
145 <ul>
146 <li> auto: Automatically guess sequence type from the data
147 </li><li> protein
148 </li><li> dna
149 </li><li> rna
150 </li>
151 </ul>
152
153 <h4>Ignore lower case</h4>
154 Disregard lower case letters in the and only count
155 upper case letters in sequences?
156
157 <h4>Units</h4>
158 The units used for the y-axis.
159 <ul>
160 <li> probability: Show residue probabilities, rather than information content. If <a href="#CA">compositional adjustment</a> is disabled, then these are the raw residue frequencies.
161 </li><li> bits: Information content in bits
162 </li><li> nats: Natural units, 1 bit = ln 2 (0.69) nats
163 </li><li> kT : Thermal energy units in natural units (Numerically the same as nats)
164 </li><li> kJ/mol : Thermal energy (Assuming T = 300 K)
165 </li><li> kcal/mol : Thermal energy (Assuming T = 300 K)
166 </li>
167 </ul>
168
169
170 <h4>First position number</h4>
171 The numerical label of the first residue in the multiple sequence alignment. The label must be an integer. Residue labels for the logo will be relative to this number. (See also: Logo Range)
172 <h4>Logo range</h4>
173 By default, all sequence data is displayed in the Sequence Logo. With this option, you can instead show a subrange of the entire sequence. Start and end positions are included, and the numbering of positions is relative to the sequence number of the first position. (See also: 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 will be displayed, and they will be numbered "5", "6", "7", "8", "9" and "10".
174
175 <a name="CA"></a>
176 <h4>Composition</h4>
177 <p>
178 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, insists on equiprobable background distributions, or turn off composition adjustment altogether.
179 </p>
180 <p>
181 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.
182 </p>
183 <p>
184 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).
185 </p>
186 <p>
187 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.
188 </p>
189
190 <h4>Scale stack width</h4>
191 Scale the visible stack width by the fraction of symbols in the column? (i.e. columns with many gaps or unknown residues are narrow.)
192
193 <h4>Error bars</h4>
194 Display error bars. These indicate an approximate, Bayesian 95% confidence interval.
195
196 <h4>Title</h4>
197 Give your logo a title.
198
199 <h4>Figure label</h4>
200 An optional figure label, added to the top left (e.g. '(a)')
201
202 <h4>X-axis</h4>
203 Add a label to the x-axis, or hide axis altogether.
204
205 <h4>Y-axis</h4>
206 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.
207
208 <h4>Y-axis scale</h4>
209 The height of the y-axis in designated units. The automatic option will pick reasonable defaults based on the sequence type and axis unit.
210
211 <h4>Y-axis tic spacing</h4>
212 The distance between major tic marks on the Y-axis.
213
214 <h4>Sequence end labels</h4>
215 Choose this option to label the 5' &amp; 3' ends of nucleic acid or the N &amp; C termini of amino acid sequences.
216
217 <h4>Version fineprint</h4>
218 Toggle display of the CodonLogo version information in the lower right corner.
219
220 <h4>Color Scheme</h4>
221 <ul>
222 <li> auto : use Base Pairing for nucleic acids (NA), Hydrophobicity for amino acids (AA).
223 </li><li> monochrome: All symbols black
224 </li><li> Base Pairing (NA default) :
225 <table border="1" cellpadding="2" cellspacing="0" >
226 <tr><td>2 Watson-Crick hydrogen bonds</td><td>TAU</td><td style="color:darkorange">dark orange</td></tr>
227 <tr><td>3 Watson-Crick hydrogen bonds</td><td>GC</td><td style="color:blue"> blue</td></tr>
228 </table>
229
230 </li><li> Classic (NA) : WebLogo (version 1 and 2) and makelogo default color scheme for nucleic acids: G, orange; T &amp; U, red; C, blue; and A, green.
231 <table border="1" cellpadding="2" cellspacing="0" >
232 <tr><td>G</td><td style="color:orange"> orange</td></tr>
233 <tr><td>TU</td><td style="color:red"> red</td></tr>
234 <tr><td>C</td><td style="color:blue">blue</td></tr>
235 <tr><td>A</td><td style="color:green">green</td></tr>
236 </table>
237
238 </li><li> Hydrophobicity (AA default) :
239 <table border="1" cellpadding="2" cellspacing="0" >
240 <tr><td>Hydrophobic</td><td>RKDENQ</td><td style="color:black"> black</td></tr>
241 <tr><td>Neutral</td><td>SGHTAP</td><td style="color:green"> green</td></tr>
242 <tr><td>Hydrophilic</td><td>YVMCLFIW</td><td style="color:blue">blue</td></tr>
243 </table>
244
245 </li><li> Chemistry (AA): Color amino acids according to chemical properties. WebLogo (version 1 and 2) and makelogo default color.
246 <table border="1" cellpadding="2" cellspacing="0" >
247 <tr><td>Polar</td><td>G,S,T,Y,C,Q,N</td><td style="color:green"> green</td></tr>
248 <tr><td>Basic</td><td>K,R,H</td><td style="color:blue"> blue</td></tr>
249 <tr><td>Acidic</td><td>D,E</td><td style="color:red">red</td></tr>
250 <tr><td>Hydrophobic</td><td>A,V,L,I,P,W,F,M</td><td style="color:black">black</td></tr>
251 </table>
252
253 </li><li> Charge (AA) :
254 <table border="1" cellpadding="2" cellspacing="0" >
255 <tr><td>Positive</td><td>KRH</td><td style="color:blue"> blue</td></tr>
256 <tr><td>Negative</td><td>DE</td><td style="color:red"> red</td></tr>
257 </table>
258
259
260
261
262 </li><li> Custom : 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.)
263 </li>
264 </ul>
265
266 <h4>More Options</h4>
267 The CodonLogo <a href="#CLI">command line client</a>, <code>codonlogo</code>, provides many more options and greater control over the final logo appearance.
268
269
270
271
272
273
274 <!-- ========================================================= -->
275 <a name="download" ></a>
276 <h2>Installing CodonLogo</h2>
277
278
279 <h4>Dependencies</h4>
280 <p>
281 CodonLogo is written in python. It is necessary to have <a href="http://www.python.org/download/">python 2.3, 2.4 or 2.5</a> and the
282 extension packages <a href="http://www.scipy.org/Download">numpy</a> and
283 <a href="http://code.google.com/p/corebio">corebio</a>
284 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.
285 </p>
286
287 <!--
288 <h4> Download and Installation</h4>
289 <p>
290 If the python package <a href="http://peak.telecommunity.com/DevCenter/setuptools"><code>setuptools</code></a> has been installed, then WebLogo and its dependancies can be downloaded and installed with a single command:
291 <pre>
292 sudo easy_install weblogo
293 </pre>
294 </p>-->
295 <!--
296 <p>
297 Alternatively, CodonLogo and its dependancies can be installed manually.
298 The CodonLogo source code can be downloaded from
299 <a href="http://code.google.com/p/weblogo/">http://code.google.com/p/weblogo/</a>.
300 This code is distributed under various <a href="http://www.opensource.org/docs/definition">open source licenses</a>. Please consult the <code>LICENSE.txt</code> file in the source distribution for details.
301 </p>-->
302
303 <p>
304 After unpacking the CodonLogo tarfile, it should be possible to immediately create
305 logos using the command line client (Provided that python, numpy, corebio and ghostscript have already been installed).
306 </p>
307 <pre>
308 ./codonlogo --format PNG &lt; htdocs/examples/cap_hth.fa &gt; cap_hth.png
309 </pre>
310 <p>
311 Please consult the file <code>build_examples.sh</code> for more examples.
312 </p><p>
313 To run CodonLogo as a stand alone web service, run the logo server command :
314 </p>
315 <pre>
316 ./codonlogo --serve
317 </pre>
318 <p>
319 It should now be possible to access CodonLogo at <a href="http://localhost:8080/">http://localhost:8080/</a>.
320 </p>
321
322 <p>
323 The command line client and WebLogo libraries can be permanently installed using the supplied <code>setup.py</code> script.
324 <pre>
325 sudo python setup.py install
326 </pre>
327 Run <code>python setup.py help</code> for more installation options. For example, to specifically install the CodonLogo script to /usr/local/bin
328 <pre>
329 sudo python setup.py install_scripts --install-dir /usr/local/bin
330 </pre>
331 </p>
332
333
334 </p>
335 <h4>Web App</h4>
336
337 <p>
338 To use CodonLogo as a web application, first install the weblogo dependancies and libraries as above, then
339 place (or link) the <code>weblogolib/weblogo_htdocs</code> directory
340 somewhere within the document root of your webserver. The webserver
341 must be able to execute the CGI script <code>create.cgi</code>. For Apache, you may have to add an <code>ExecCGI</code>
342 option and add a cgi handler in the <code>httpd.conf</code> configuration file.
343 Something like this:
344 </p>
345 <pre>
346 &lt;Directory "/home/httpd/htdocs/weblogo/">
347 Options FollowSymLinks MultiViews ExecCGI
348 AllowOverride None
349 Order allow,deny
350 Allow from all
351 &lt;/Directory>
352 ...
353 # To use CGI scripts outside of ScriptAliased directories:
354 # (You will also need to add "ExecCGI" to the "Options" directive.)
355 #
356 AddHandler cgi-script .cgi
357 </pre>
358 It may also be necessary to set the <code>PATH</code> and <code>PYTHONPATH</code> environment variables.
359 <pre>
360 SetEnv PYTHONPATH /path/to/weblogo/libraries
361 </pre>
362 The cgi script also has to be able to find the '<code>gs</code>' ghostscript executable. If ghostscipt is installed in a non-standard location add the following environment variable.
363 <pre>
364 SetEnv COREBIOPATH /path/to/gs
365 </pre>
366 The maxium bytes of uploaded sequecne data can be controlled with the <code>WEBLOGO_MAX_FILE_SIZE</code> environment variable.
367 <pre>
368 SetEnv WEBLOGO_MAX_FILE_SIZE 1000000
369 </pre>
370
371
372
373
374 <!-- ================================================================== -->
375 <a name="CLI" ></a>
376 <h2><code>codonlogo</code>, The CodonLogo Command Line Interface (CLI)</h2>
377 The command line client has many options not available through the web interface. Please consult the bundled <code>build_examples.sh</code> script for inspiration.
378 <pre >
379 Usage: codonlogo [options] < sequence_data.fa > sequence_logo.eps
380
381 Create sequence logos from biological sequence alignments.
382
383 Options:
384 --version show program's version number and exit
385 -h --help show this help message and exit
386
387 Input/Output Options:
388 -f --fin FILENAME Sequence input file (default: stdin)
389 --fin-format FORMAT Multiple sequence alignment format: (clustal,
390 fasta, plain, msf, genbank, nbrf, nexus,
391 phylip, stockholm, intelligenetics, table,
392 array)
393 -o --fout FILENAME Output file (default: stdout)
394 -F --format FORMAT Format of output: eps (default), png,
395 png_print, pdf, jpeg, txt
396
397 Logo Data Options:
398 -A --sequence-type TYPE The type of sequence data: 'protein', 'rna' or
399 'dna'.
400 -a --alphabet ALPHABET The set of symbols to count, e.g. 'AGTC'. All
401 characters not in the alphabet are ignored. If
402 neither the alphabet nor sequence-type are
403 specified then weblogo will examine the input
404 data and make an educated guess. See also
405 --sequence-type, --ignore-lower-case
406 --ignore-lower-case YES/NO
407 Disregard lower case letters and only count
408 upper case letters in sequences? (Default: No)
409 -U --units NUMBER A unit of entropy ('bits' (default), 'nats',
410 'digits'), or a unit of free energy ('kT',
411 'kJ/mol', 'kcal/mol'), or 'probability' for
412 probabilities
413 --composition COMP. The expected composition of the sequences:
414 'auto' (default), 'equiprobable', 'none' (Do
415 not perform any compositional adjustment), a
416 CG percentage, a species name (e.g. 'E. coli',
417 'H. sapiens'), or an explicit distribution
418 (e.g. {'A':10, 'C':40, 'G':40, 'T':10}). The
419 automatic option uses a typical distribution
420 for proteins and equiprobable distribution for
421 everything else.
422 --weight NUMBER The weight of prior data. Default: total
423 pseudocounts equal to the number of monomer
424 types.
425 -i --first-index INDEX Index of first position in sequence data
426 (default: 1)
427 -l --lower INDEX Lower bound of sequence to display
428 -u --upper INDEX Upper bound of sequence to display
429
430 Logo Format Options:
431 These options control the format and display of the logo.
432
433 -s --size LOGOSIZE Specify a standard logo size (small, medium
434 (default), large)
435 -n --stacks-per-line COUNT Maximum number of logo stacks per logo line.
436 (default: 40)
437 -t --title TEXT Logo title text.
438 --label TEXT A figure label, e.g. '2a'
439 -X --show-xaxis YES/NO Display sequence numbers along x-axis?
440 (default: True)
441 -x --xlabel TEXT X-axis label
442 -S --yaxis UNIT Height of yaxis in units. (Default: Maximum
443 value with uninformative prior.)
444 -Y --show-yaxis YES/NO Display entropy scale along y-axis? (default:
445 True)
446 -y --ylabel TEXT Y-axis label (default depends on plot type
447 and units)
448 -E --show-ends YES/NO Label the ends of the sequence? (default:
449 False)
450 -P --fineprint TEXT The fine print (default: weblogo version)
451 --ticmarks NUMBER Distance between ticmarks (default: 1.0)
452 --errorbars YES/NO Display error bars? (default: True)
453
454 Color Options:
455 Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc.
456
457 -c --color-scheme SCHEME Specify a standard color scheme (auto, base
458 pairing, charge, chemistry, classic,
459 hydrophobicity, monochrome)
460 -C --color COLOR SYMBOLS DESCRIPTION
461 Specify symbol colors, e.g. --color black AG
462 'Purine' --color red TC 'Pyrimidine'
463 --default-color COLOR Symbol color if not otherwise specified.
464
465 Advanced Format Options:
466 These options provide fine control over the display of the logo.
467
468 -W --stack-width POINTS Width of a logo stack (default: 10.8)
469 -H --stack-height POINTS Height of a logo stack (default: 54.0)
470 --box YES/NO Draw boxes around symbols? (default: no)
471 --resolution DPI Bitmap resolution in dots per inch (DPI).
472 (default: 96 DPI, except png_print, 600 DPI)
473 Low resolution bitmaps (DPI<300) are
474 antialiased.
475 --scale-width YES/NO Scale the visible stack width by the fraction
476 of symbols in the column? (i.e. columns with
477 many gaps of unknowns are narrow.) (default:
478 yes)
479 --debug YES/NO Output additional diagnostic information.
480 (default: False)
481
482 CodonLogo Server:
483 Run a standalone webserver on a local port.
484
485 --serve Start a standalone CodonLogo server for creating
486 sequence logos.
487 --port PORT Listen to this local port. (Default: 8080)
488 </pre >
489 <!-- ===================================================================== -->
490 <a name="API" ></a>
491 <h2>WebLogo Application Programmer Interface (API)</h2>
492
493 The WebLogo python libraries provide even greater flexibility than the command line client. The code is split between two principle packages, <code>weblogo</code> itself, which contains specialized sequence logo generation code, and <code>corebio</code>, a package that contains code of more general utility.
494 Please consult the <a href="http://weblogo.googlecode.com/svn/trunk/apidocs/index.html">WebLogo</a> and <a href="http://corebio.googlecode.com/svn/tags/0.5.0/apidocs/index.html">CoreBio</a> API documentation.
495
496
497
498 <!-- ================================================================== -->
499 <a name="dev" ></a>
500 <h2>WebLogo Development and Future Features</h2>
501 <p>
502 The development project is hosted at
503 <a href="http://code.google.com/p/weblogo/">http://code.google.com/p/weblogo</a>.
504
505 If you wish to extend WebLogo or to contribute code, then you should download the full source code development package directly from the subversion repository.
506 </p>
507 <pre>
508 &gt; svn checkout http://weblogo.googlecode.com/svn/trunk/ weblogo
509 &gt; cd weblogo
510 &gt; ./weblogo &lt; cap.fa &gt; cap.eps
511 </pre>
512 <p>
513 Please consult the developer notes, <code>DEVELOPERS.txt</code> and software license <code>LICENSE.txt</code>
514 </p>
515
516 <p> Outstanding bugs and feature requests are listed on the <a href="http://code.google.com/p/weblogo/issues/list">WebLogo issue tracker.</a>
517 </p>
518
519 <a name="misc" ></a>
520 <h2>Miscellanea</h2>
521 <h4> Release Notes and Known Bugs</h4>
522 The <a href="weblogo_changelog.txt">WebLogo release notes</a> detail changes to WebLogo and known issues with particular versions.
523
524 <h4>WebLogo 2</h4>
525 The legacy WebLogo 2 sever can be found <a href="http://weblogo.berkeley.edu/">here.</a>
526
527
528
529 <h4>Acknowledgments</h4>
530
531 <p>
532 WebLogo was created by
533 <a href="http://threeplusone.com/">Gavin E. Crooks</a>,
534 <a href="http://compbio.berkeley.edu/">Liana Lareau</a>,
535 <a href="http://compbio.berkeley.edu/">Gary Hon</a>,
536 <a href="http://compbio.berkeley.edu/">John-Marc Chandonia</a> and
537 <a href="http://compbio.berkeley.edu/people/brenner/">Steven E. Brenner</a>.
538 <a href="weblogo_changelog.txt">Many others</a> have provided suggestions, bug fixes and moral support.
539 </p>
540
541 <p>
542 WebLogo was originally based upon the programs
543 <a href="http://www.lecb.ncifcrf.gov/~toms/delila/alpro.html">alpro</a> and
544 <a href="http://www.lecb.ncifcrf.gov/~toms/delila/makelogo.html">makelogo</a>,
545 both of which are part of Tom Schneider's
546 <a href="http://www.lecb.ncifcrf.gov/~toms/delila.html">delila</a> package. Many thanks
547 are due to him for making this software freely available and for encouraging its use.
548 </p>
549
550
551
552
553
554 </td></tr>
555 </table>
556
557
558 <script type="text/javascript">
559 var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
560 document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
561 </script>
562 <script type="text/javascript">
563 var pageTracker = _gat._getTracker("UA-5951066-1");
564 pageTracker._trackPageview();
565 </script>
566 </body>
567 </html>
568
569
570
571
572
573
574
575
576