Summary: To improve the quality of ChIP data, ChIP-chip is being replaced by ChIP-seq. This new technology offers higher resolution and lower background for transcription factor binding site identification. Therefore, in Chapter 3, I wrote a four-step algorithm to infer true transcription factor binding sites from ChIP-seq data. This algorithm accounts for peak representation on both DNA strands, reproducibility of peaks, and the presence of a motif. This algorithm was written for the genomic toolkit Galaxy. Steps in the algorithm, when possible, were written using preexisting tools on Galaxy. When not possible, certain steps were written in Python. This algorithm is freely available at http://dancluster.g2.bx.psu.edu.