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This article introduces the relevant knowledge of "how to use MEME-ChIP to mine de novo motif in a sequence". In the operation of actual cases, many people will encounter such a dilemma, so let the editor lead you to learn how to deal with these situations. I hope you can read it carefully and be able to achieve something!

MEME-ChIP is a comprehensive motif analysis software that integrates the following software

MEME

DREME

CentriMo

Tomtom

FIMO

SpaMo

It is suitable for analyzing motif information on sequences with a large amount of data. First, the de novo motif is predicted by MEME and DREME software, and then the motif which is significantly enriched in the central region of the sequence is identified by CentriMo. At the same time, the predicted de novo motif is compared with the known motif in the specified database by Tomtom software to determine the similarity between them. Finally, the binding site of motif on the input sequence was predicted by FIMO software.

The URL of the online tool is as follows

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

You only need to provide the input sequence.

By default, the sequences of the upstream and downstream 50bp in the central area of the input sequence are automatically extracted for subsequent analysis, because the DREME software works best for sequences with a length of about 100bp.

The output is as follows

The first column is the sequence logo corresponding to motif, the second is the software that identifies the corresponding motif, the third is the E value corresponding to motif, the fourth is the known motif obtained by Tomtom alignment, the fifth is the distribution of motif binding sites on the input sequence obtained by Centrimo analysis, and the last is the analysis results of SpaMo and FIMO software, in which the GFF3 file is saved in the motif binding site on the input sequence.

The basic usage of the command line version is as follows

Meme-chip\

-meme-p 6\

-oc out_dir\

-db JASPAR2018_CORE_non-redundant.meme\

Input.fna

The-meme-p specifies the number of threads running MEME, the running speed of the MEME software slows down, and multithreading can improve the running speed. The-db parameter specifies the database of the known motif. The motif database is available for download on the official website of the software.

Compared with MEME and DREME, MEME-ChIP is more powerful.

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