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This article focuses on "how to use WebLogo to visualize motif", interested friends may wish to take a look. The method introduced in this paper is simple, fast and practical. Now let the editor take you to learn how to use WebLogo to visualize motif.

WebLogo is a classic motif visualization software, in many articles have mentioned the use of this software to draw motif sequence logo. As an online tool, it is easy to operate and easy to use.

Http://weblogo.threeplusone.com/

You only need the result of multiple sequence alignment of the uploaded sequence. The sequence of bing sites in the following figure is an example.

1. Upload multiple sequence alignment results

Click the create menu to upload the result of multiple sequence alignment in fasta format

The result of multiple sequence alignment in the example is as follows

> binding_site1

CCCATTGTTCTC

> binding_site2

TTTCTGGTTCTC

> binding_site3

TCAATTGTTTAG

> binding_site4

CTCATTGTTGTC

> binding_site5

TCCATTGTTCTC

> binding_site6

CCTATTGTTCTC

> binding_site7

TCCATTGTTCGT

> binding_site8

CCAATTGTTTTG2. Adjust parameter settin

It is divided into two parts. the first part mainly adjusts the format of the output file as follows

You can set the title, output file format, support PNG,PDF,SVG,JPEG and other formats. The input sequence type will be judged automatically, and dan, rna and protein3 sequences are supported.

The second part mainly adjusts the content displayed on the picture, as shown below.

In general, you need to remove error bar and version information. The main adjustment in this part is the color matching. For DNA and RNA, the built-in color matching is as follows

For protein sequences, the built-in color matching is as follows

After the settings have been adjusted, click Create WebLogo. The DNA sequence in the example uses classic color matching, and the result is as follows

WebLogo also has a corresponding command line version, which can be run locally. The basic usage is as follows

Weblogo-format PNG

Cap.png

Please refer to the help documentation on the official website for more parameters and details.

At this point, I believe you have a deeper understanding of "how to use WebLogo to visualize motif". You might as well do it in practice. Here is the website, more related content can enter the relevant channels to inquire, follow us, continue to learn!

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