Recent studies have shown that conceptual and structural characteristics of a website can play an important role in the quality of recommendations provided by a recommendation system. Resources like Google Directory, Yahoo! Directory and web-content management systems attempt to organize content conceptually. Most recommendation models are limited in their ability to use this domain knowledge. We propose a novel technique to incorporate the conceptual characteristics of a website into a usage-based recommendation model. We use a framework based on biological sequence alignment. Similarity scores play a crucial role in such a construction and we introduce a scoring system that is generated from the website’s concept hierarchy. These scores fit seamlessly with other quantities used in similarity calculation like browsing order and time spent on a page. Additionally they demonstrate a simple, extensible system for assimilating more domain knowledge. We provide experimental results to illustrate the benefits of using concept hierarchy.