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This article shows you how to use DREME to mine the de novo motif in the sequence, the content is concise and easy to understand, it can definitely brighten your eyes. I hope you can get something through the detailed introduction of this article.

DREME is also a commonly used de novo motif analysis software, it has the following characteristics

Only motif analysis of nucleic acid sequences, that is, DNA and RNA sequences, is supported. Amino acid sequences are not supported.

DREME needs two sets of sequences, one of which is control. The main function is to mine the motif that is relatively enriched in the other set compared with control.

The sequence set corresponding to contorl is called negative sequences, and the other group is called positive sequences. Fisher's exact test is used to analyze whether motif appears more times in positive than in negative.

If you provide only one sequence set, use base random sampling to simulate a set of contorl sequences based on the sequence you provide. the sequence set constructed in this way is also called shuffled sequences.

The URL of the online tool is as follows

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

It is OK to provide a set of control and input sequences at the same time. It should be noted that the number of sequences in the two sets must be the same, and the length of the sequence is the best around 100bp. It is usually possible to use the sequences of the upstream and downstream 50bp of the peak center.

The output is as follows

At the same time, the motif is found on the input sequence and its reverse complementary chain, and the RC Logo in the output represents the motif on the reverse complementary chain. Click on each More to view the specific information of each motif, as shown below

The statistics of the number of the motif and the corresponding base combinations in the two sequence sets and the corresponding p value and other information are given. It should be noted that the number statistics here is not a simple statistics of the number of the character in the input sequence, and it is an independent operation when analyzing the total motif and the corresponding number of base combinations, so it does not mean that the number of each base combination is the total number of motif.

The basic usage of the command line version of DREME is as follows

Dreme-oc out_dir-png-p input.fa

DREME is suitable for finding motif whose length is between 3 and 8bp, while the motif length of MEME can be adjusted by parameters, so it can be applied more widely.

The above is how to use DREME to mine de novo motif in a sequence. Have you learned any knowledge or skills? If you want to learn more skills or enrich your knowledge reserve, you are welcome to follow the industry information channel.

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