On 2017 Nov 29, Michael Hoffman commented:

I read this paper with interest and welcome its innovative new experimental method.

Readers may be interested in our 2016 preprint, "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet" (Viner et al. 2016, bioRxiv, https://doi.org/10.1101/043794). In our paper, we also extended the four-symbol DNA alphabet to include additional symbols for methyl-C and guanine paired to methyl-C, and used position weight matrices (PWMs) based on this expanded alphabet. Our paper also used sequence logos with the expanded alphabet. The use of an expanded epigenetic alphabet for an energy PWM (ePWM) in the 2017 Zuo et al. paper is an interesting development.

In 2015, we added custom alphabet support to most tools in the MEME Suite to allow use of this expanded alphabet. We hope that those tools will be useful for many.

On 2017 Nov 29, Michael Hoffman commented:

I read this paper with interest and welcome its innovative new experimental method.

Readers may be interested in our 2016 preprint, "Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet" (Viner et al. 2016, bioRxiv, https://doi.org/10.1101/043794). In our paper, we also extended the four-symbol DNA alphabet to include additional symbols for methyl-C and guanine paired to methyl-C, and used position weight matrices (PWMs) based on this expanded alphabet. Our paper also used sequence logos with the expanded alphabet. The use of an expanded epigenetic alphabet for an energy PWM (ePWM) in the 2017 Zuo et al. paper is an interesting development.

In 2015, we added custom alphabet support to most tools in the MEME Suite to allow use of this expanded alphabet. We hope that those tools will be useful for many.