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
|
.. WebLogo documentation master file, created by
sphinx-quickstart on Sat Nov 3 20:56:21 2018.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
WebLogo 3: Sequence Logos Redrawn
===================================
WebLogo is software designed to make the generation of sequence logos easy and painless. A sequence logo 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. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.
WebLogo features a web interface (http://weblogo.threeplusone.com), and a command line interface provides more options
and control (http://weblogo.threeplusone.com/manual.html#CLI). These pages document the API.
The main WebLogo webserver is located at http://weblogo.threeplusone.com
Please consult the manual for installation instructions and more information:
(Also located in the weblogolib/htdocs subdirectory.)
http://weblogo.threeplusone.com/manual.html
For help on the command line interface run
.. code-block:: console
weblogo --help
To build a simple logo run
.. code-block:: console
weblogo < cap.fa > logo0.eps
To run as a standalone webserver at localhost:8080
.. code-block:: console
weblogo --serve
Distribution and Modification
-----------------------------
This package is distributed under the MIT Open Source License.
Please see the LICENSE.txt file for details on copyright and licensing.
The WebLogo source code can be downloaded from
https://github.com/WebLogo/weblogo
WebLogo requires Python 3.6 or 3.7. Generating logos in PDF or bitmap graphics formats
require that the ghostscript
program 'gs' be installed. Scalable Vector Graphics (SVG) format also requires
the program 'pdf2svg'.
.. contents:: :local:
.. currentmodule:: weblogo
.. toctree::
:maxdepth: 3
:caption: Contents:
intro
seq
seq_io
logo
formatting
* :ref:`genindex`
* :ref:`modindex`
|
