RINQ: Reference-based Indexing for Network Queries.

ABSTRACT: We consider the problem of similarity queries in biological network databases. Given a database of networks, similarity query returns all the database networks whose similarity (i.e. alignment score) to a given query network is at least a specified similarity cutoff value. Alignment of two networks is a very costly operation, which makes exhaustive comparison of all the database networks with a query impractical. To tackle this problem, we develop a novel indexing method, named RINQ (Reference-based Indexing for Biological Network Queries). Our method uses a set of reference networks to eliminate a large portion of the database quickly for each query. A reference network is a small biological network. We precompute and store the alignments of all the references with all the database networ

SUBMITTER: Gulsoy G 

PROVIDER: S-EPMC3117351 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature