for example, is there any tool I can use to calculate and predict the causation relating to 2 specific genes!
Dear Omar Samir
DNA footprinting is an in vitro method used to investigate protein binding to particular sections of DNA. This method smartly takes use of the fact that when a transcription factor binds to DNA with a specific affinity, the DNA is protected against destruction by nucleases.
Transcription factors bind to chromatin's cis-regulatory sequences. The protein is cross-linked to DNA and the chromatin is sheared to determine the genomic loci bound.
The main method for predicting transcription factor binding sites is to scan a DNA sequence of interest using a position weight matrix (PWM) for a transcription factor of interest, and several pattern-matching algorithms have been developed for this purpose.
A protein must have two characteristics in order to be classified as a transcription factor. 1) The ability to bind to DNA and 2) to recruit RNA polymerase/alter gene transcription.
Kind Regards
Qamar Ul Islam
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