Prediction of Specific DNA-Binding Residues in a Transcription Factor based on Analysis of the Polypeptide Sequence
Date Issued
2008
Date
2008
Author(s)
Chu, Wen-Yi
Abstract
This thesis presents the design of a polypeptide sequence based predictor aiming to identify the residues in a transcription factor that are involved in specific binding with the DNA. As a recent study has revealed that the tertiary structures of a large number of transcription factors are mostly disordered, the capability to identify the residues in a transcription factor that play key roles in interaction with the DNA based purely on analysis of the polypeptide sequence is highly desirable. In this respect, it is further desirable to have a predictor capable of distinguishing those residues involved in specific binding with the DNA, since specific binding corresponds to sequence-specific recognition of a gene, which is essential for correct gene regulation. The design of the proposed predictor is distinctive by employing a hybrid approach. That is, two prediction mechanisms specialized for making predictions in different types of protein secondary structures have been incorporated. In the experiments reported in this thesis, the proposed hybrid predictor delivered precision of 77.4%, sensitivity of 59.5%, and specificity of 98.8%
Subjects
secific-binding residue
transcription factor
Type
thesis
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