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How to use motif analysis comprehensive tool MEME, many novices are not very clear about this, in order to help you solve this problem, the following editor will explain in detail for you, people with this need can come to learn, I hope you can gain something.

MEME is a toolkit for motif analysis, providing a variety of related tools

According to the purpose and function of the analysis, the related tools are divided into the following four categories

1. Motif Discovery

This part of the tool is used to predict the motif information on the input sequence, and supports DNA,RNA or protein sequence. The corresponding function is called de novo motif discovery. The list of tools is as follows.

MEME

DREME

MEME-ChIP

GLAM2

MoMo

The common application scenario is to mine the pattern features in these sequences according to the peak sequences obtained from chip_seq and other data. Taking MEME as an example, the output is illustrated as follows

2. Motif Enrichment

This part of the tool is used to analyze the known enrichment of motif on the input sequence, and the list of tools is as follows

CentriMo

AME

SpaMo

GOMo

The common application scenario is to analyze the known motif enriched in these sequences according to the peak sequences of ATAC_seq. Taking CentriMo as an example, the output is illustrated as follows

3. Motif Scanning

This part of the tool is used to analyze the possible locations of motif on the input sequence, and the list of tools is as follows

FIMO

MAST

MCAST

GLAM2SCan

The common application scenario is to analyze whether there is a corresponding binding site in the promoter sequence of a gene according to the motif of transcription factors. Taking FIMO as an example, the output is illustrated as follows

4. Motif Comparison

This part of the tool is used to compare the similarities between different motif, including the Tomtom tool. Motif contains both consistency sequence and PFM matrix information. With the help of this tool, we can effectively judge the similarity between two motif. The classic application scenario is to analyze and compare the analyzed de novo motif with a known motif database to find similar motif. The output is shown below.

MEME provides both online version and local version, which is powerful and easy to use at the same time, so it is a sharp tool for motif analysis.

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