Looking for transcription factor binding sites
Document typeMaster thesis
Rights accessRestricted access - confidentiality agreement
Transcription factors are proteins involved in the regulation of DNA transcription. Indeed they are the proteins which enable or disable the RNA-polymerase production. In order to do so, transcription factors are bound at some specific zones of the DNA called transcription factor binding sites (TFBS). Since transcription factors and RNA-polymerase production are related to many pathologies, such as cancer, finding TFBS on DNA sequences for some given transcription factor has become one of the fundamental problems in bioinformatics. The main goal of this work is to adapt the algebraic geometry tools used in phylogenetics to the TFBS problem and study this problem through the tools obtained from there. Additionaly, we will also study a numerical approach via the Expectation Maximization algorithm.