-Authors: Zaslavsky, Elena (2006)
A major objective in molecular biology is to understand how a genome encodes the information that speci es when and where a gene will be transcribed into its protein product. Mediating proteins, known as transcription factors, facilitate this process by interacting with the cell 's sDNA and the transcription machinery. It is of central importance to identify all sequence-speci c DNA binding sites of transcription factors. In this thesis, we consider two relevant computational problems.
The first problem is to develop a representation for a group of known binding sites of a particular transcription factor, in order to facilitate recognition of other binding sites of the same protein. We evaluate the e ectiveness of several approaches commonly used for this problem, and show that the... 
