Spring 2008 Database Seminar

Thursday Apr. 17th, 2008
CSE Room 305
12:00 - 1:00pm

Consistent alignment of metabolic pathways without abstraction
Ferhat Ay

Similarities between biological pathways indicate important functional similarities that are hard to identify by comparing the individual entities. Existing methods, often, try to address metabolic pathway alignment problem by ignoring all the entities except for one type. This kind of abstraction, however, reduces the relevance of the alignment significantly as it can cause massive losses in the information content. We consider the pairwise alignment problem for metabolic pathways. One distinguishing feature of our method is that it aligns reactions, compounds and enzymes without any abstraction of pathways. We pursue the intuition that both pairwise similarities of entities and the similarities of their neighborhood are crucial in aligning these entities. Hence, we account for the effect of pairwise similarities (homology) and the effect of organization of pathways (topology) in our algorithm. Our experiments show that, our method finds biologically and statistically significant alignments in less than a second for pathways with ~100 entities.

For upcoming talks, visit http://www.cise.ufl.edu/dbcenter/seminar.shtml.