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ddG LogoGenerator

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lenail:
'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,

xiangjun:

--- Quote ---'m curious about the math behind PWM logos with ddG on the y axis.
--- End quote ---

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" informative, especially the summary post at the end from Dr. Bussemaker.


--- Quote ---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)?

--- End quote ---


With a PWM, you could run Convert2PSAM to transform it into a pseudo-PSAM, and then call LogoGenerator.

HTH,

Xiang-Jun

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