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Editor to share with you what the PFM matrix in motif is like. I hope you will get something after reading this article. Let's discuss it together.

PFM, whose full name is position frequency matrix, is used to represent the base distribution frequency of motif. It is an easy concept in itself to understand. The motif sequence shown in the following figure is an example.

The corresponding base distribution frequency can be calculated according to the above 8 sequences, as shown below.

One base per behavior, each listed as a position of motif.

In addition to consistency sequences and sequence logo, the PFM matrix is also a common element when describing motif information. Different software will have different standards, and understanding these formats is the core of this article.

JASPAR is a commonly used transcription factor motif database, in which there are several formats for the PFM matrix, as shown in the following figure

1. RAW PFM

The original PFM matrix is illustrated as follows

The first line is similar to the sequence identifier in fasta format, starting with >. The string that begins with MA is the number of the transcription factor in the JASPAR database and is unique, and AGL3 represents the name of the transcription factor.

The next four lines represent the frequency distribution of A, C, G and T bases at each position in turn.

2. JASPAR

The PFM matrix in JASPAR format is illustrated as follows

It is very similar to the original PFM matrix, except that the corresponding base is marked at the beginning of each line and the base frequency matrix is enclosed with the [and] operator.

3. TRANSFAC

The PFM matrix in TRANSFAC format is illustrated as follows

The file standard in the TRANSFAC database is adopted. AC represents the motif number, ID represents the name of motif, PO and the base distribution frequency corresponding to the following behavior.

4. MEME

The PFM matrix in MEME format is illustrated as follows

ALPJABEAT represents the character set of bases, strands represents the direction of the chain, +-ghostwriter does not specify the direction of the chain when using meme to predict motif, Background represents the frequency of base composition in the background, and the base distribution frequency corresponding to MOTIF and the following behaviors.

The format of PFM matrix corresponding to different software and database is different, which should be paid attention to when using different software and database.

After reading this article, I believe you have a certain understanding of "what the PFM matrix is like in motif". If you want to know more about it, you are welcome to follow the industry information channel. Thank you for reading!

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