Publication Date
Fall 2013
Degree Type
Master's Project
Degree Name
Master of Science (MS)
Department
Computer Science
Abstract
Traditional Position Weight Matrices (PWMs) that are used to model Transcription Factor Binding Sites (TFBS) assume independence among different positions in the binding site. In reality, this may not necessarily be the case. A better way to model TFBS is to consider the distribution of dinucleotides or trinucleotides instead of just mononucleotides, thus taking neighboring nucleotides into account. We can therefore, extend the single nucleotide PWM to a dinucleotide PWM or an even higher-order PWM to correctly estimate the dependencies among the nucleotides in a given sequence. The purpose of this project is to develop an algorithm to implement higher-order PWMs to detect the TFBS and other biological motifs in DNA, RNA, and proteins.
Recommended Citation
Srinivasan, Dhivya, "Higher Order PWM for Modeling Transcription Factor Binding Sites" (2013). Master's Projects. 327.
DOI: https://doi.org/10.31979/etd.yvas-9f4b
https://scholarworks.sjsu.edu/etd_projects/327
