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Author Topic: ddG LogoGenerator  (Read 124441 times)

lenail

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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,
« Last Edit: October 24, 2024, 11:20:00 pm by xiangjun »
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xiangjun

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Re: ddG LogoGenerator
« Reply #1 on: July 12, 2019, 06:17:36 pm »
Quote
'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" 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)?


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

HTH,

Xiang-Jun
« Last Edit: October 24, 2024, 11:18:50 pm by xiangjun »
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