REDUCE Suite
General Category => General Discussion => Topic started by: lenail on July 12, 2019, 11:13:01 am
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'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,
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'm curious about the math behind PWM logos with ddG on the y axis.
The ddG is calculated from PSAM via a simple log-transformation. See the source code in file LogoGenerator.c. You may find the thread "IC from PSAM (http://reducesuite.bussemakerlab.org/general-discussion/ic-from-psam/)" informative, especially the summary post at the end from Dr. Bussemaker.
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)?
With a PWM, you could run Convert2PSAM to transform it into a pseudo-PSAM, and then call LogoGenerator.
HTH,
Xiang-Jun