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General Discussion / ddG LogoGenerator
« on: July 12, 2019, 11:13:01 am »
'm curious about the math behind PWM logos with ddG on the y axis.
Specifically, [http://humantfs.ccbr.utoronto.ca/]The Human Transcription Factors[/http://humantfs.ccbr.utoronto.ca/] PWM logos were generated via the REDUCE LogoGenerator, so they tell me. They have figures like this (image attached).
The LogoGenerator docs suggest I need a PSAM file or multiple sequence alignment to generate this kind of plot, but all I have is a PWM for each transcription factor.
Is it possible to generate a figure like the one above directly from a PWM? Could you point me towards a reference describing how to do this (mathematically)?
Many thanks,
Specifically, [http://humantfs.ccbr.utoronto.ca/]The Human Transcription Factors[/http://humantfs.ccbr.utoronto.ca/] PWM logos were generated via the REDUCE LogoGenerator, so they tell me. They have figures like this (image attached).
The LogoGenerator docs suggest I need a PSAM file or multiple sequence alignment to generate this kind of plot, but all I have is a PWM for each transcription factor.
Is it possible to generate a figure like the one above directly from a PWM? Could you point me towards a reference describing how to do this (mathematically)?
Many thanks,