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This article mainly introduces "how to use MEME to mine the de novo motif in the sequence". In the daily operation, I believe that many people have doubts about how to use MEME to mine the de novo motif in the sequence. Xiaobian consulted all kinds of data and sorted out simple and easy-to-use operation methods. I hope it will be helpful to answer the doubt of "how to use MEME to mine the de novo motif in the sequence". Next, please follow the editor to study!

For de novo motif analysis, we only need to provide the sequence. Because there is a certain fluctuation in the length range of peak, the peak center, that is, the sequence with fixed length on both sides of the peak, is usually selected for downstream motif analysis.

At the same time, in order to improve the operation efficiency, only part of the peak is selected for analysis, for example, the sequence of the most significant 1000 peak is selected according to the p value or enrichment factor for motif prediction. Once the input sequence is ready, you are ready for motif analysis. Meme is one of the most commonly used tools, available at

Http://meme-suite.org/tools/meme

The operation is simple, just upload the sequence, and then set a few parameter values

The output file contains the results of two parts

1. Motif

Provides motif's sequence logo, PFM, PWM matrix and other information.

2. Motif location

Provides the position information of the motif on the input sequence, as shown below

Online tools support a maximum input sequence of 80m, and larger files need local software to run. The basic usage is as follows

Meme\

Input.fna\

-oc out_dir\

-dna\

-mod zoops\

-nmotifs 3\

-revcomp

Meme's algorithm enables this tool to get both motif and motif position information on the input sequence at the same time. When outputting multiple motif, the more sites on the input sequence, the more motif priority output, so usually only need to refer to the first three motif, this tool is more suitable for scenarios with fewer types of motif, such as analyzing the chip_seq or m6A_seq data of a transcription factor.

At this point, the study on "how to use MEME to mine de novo motif in a sequence" is over. I hope to be able to solve your doubts. The collocation of theory and practice can better help you learn, go and try it! If you want to continue to learn more related knowledge, please continue to follow the website, the editor will continue to work hard to bring you more practical articles!

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