Shulou(Shulou.com)06/01 Report--

This article analyzes "how to do motif Analysis" with you. The content is detailed and easy to understand. Friends who are interested in "how to analyze motif" can follow the editor's train of thought to read it slowly and deeply. I hope it will be helpful to you after reading. Let's follow the editor to learn more about "how to do motif analysis".

In chip_seq data analysis, motif analysis is an important analysis content. Through motif analysis, we can have a better understanding of the sequence pattern of transcription factor binding sites, so what is motif?

The basic functional unit of protein is domain, which is a special three-dimensional structure. Domain with different structures specifically binds to other molecules to exert its function. Similarly, when the transcription factor binds to the DNA sequence, the sequence of its binding site is also due to certain specificity, and the pattern of the DNA sequence bound by different transcription factors is different. In order to better describe the pattern of binding site sequences, scientists put forward the concept of motif.

Motif represents the pattern of a specific base sequence. This textbook noun interpretation is not intuitive and difficult to understand. Let's look at it through an example.

The above picture shows the sequence of binding sites of a transcription factor on multiple genes. When using motif to describe the above information, the following elements are used.

1. Base frequency distribution

In the above example, the sequence length of the binding site is 12bp, and the frequency statistics of the four bases at each site are as follows.

2. Consensus sequences

A sequence is used to describe the base composition of all sequences, which is called a consistent sequence. using the IUPAC standard base representation, the bases corresponding to different letters are as follows.

The consistency sequence in the above example is as follows

3. Sequence logo

In order to describe motif more intuitively, combined with the distribution of bases in all sequences and the characteristics of consistent sequences, a representation method of sequence logo is proposed.

The base distribution frequency in the above example is plotted as follows

Similar to the stacked histogram of the frequency of base distribution at each location, sequence logo uses the following formula to calculate the height of the base at the location

The maximum value in the above formula is 2, which corresponds to the same base in all sequences, for example, the fifth position in the example is all T base. Through this representation, the distribution of bases can be highlighted as follows

It is very obvious that there are only T bases at positions 5, 8 and 9. The other locations are a mixture of several bases, and the overall height is much lower than these positions here. It is worth mentioning that we said before that the maximum value of a single base is 2, while the position of a single base in the picture above is a little smaller than 2, because it has been fine-tuned on the basis of the original formula, as shown below.

A value of e is subtracted from the original formula. In the formula for calculating the value of e, for the DNA sequence, the value of s is 4 and n represents the length of motif, which is 12 in the above example. After subtracting the e value, the maximum value is naturally smaller than 2.

There are a lot of software for motif analysis, such as meme-chip, homer and so on.

On how to conduct motif analysis to share here, I hope that the above content can make you improve. If you want to learn more knowledge, please pay more attention to the editor's updates. Thank you for following the website!

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.