A Unified Approach to Signal Detection

Two major classes of methods for finding regulatory signals are homologous and non-homologous.  Homologous will find signals by their modified or lower rate of evolution relative to a background sequence.  Non-homologous will find signals because they occur with a higher frequency than in a background sequence. These two approaches have been combined before (Wang and Stormo, 2003; Zhou and Wong, 2007).  Combining the approaches should have several advantages. Homologous detection is increasingly powerful due to the increase in know genomes.  Non-homologous analysis is powerful in making functional statements since it can compare genes with different properties or that are co-regulated.  This project proposes to unify the two approaches within the framework of statistical alignment.