Joint clustering and alignment for nucleosome occupancy analysis

Several studies show that nucleosome occupancy patterns around transcription starting sites provide evolutionary and regulatory information about genes. However, as transcription starting sites may not accurately reflect physical nucleosome occupancy patterns, clustering of nucleosome occupancy patterns centered at transcription starting sites may give rise to inaccurate and blurred cluster centers, leading to potentially inaccurate conclusions. In this paper, we propose a joint clustering and alignment method and apply it to clustering of nucleosome occupancy patterns around transcription starting sites. The experimental results using the human genome-wide data show that alignment affects the significant majority of genes and leads to more pronounced local nucleosome occupancy patterns.