GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.

ABSTRACT: Biological applications, from genomics to ecology, deal with graphs that represents the structure of interactions. Analyzing such data requires searching for subgraphs in collections of graphs. This task is computationally expensive. Even though multicore architectures, from commodity computers to more advanced symmetric multiprocessing (SMP), offer scalable computing power, currently published software implementations for indexing and graph matching are fundamentally sequential. As a consequence, such software implementations (i) do not fully exploit available parallel computing power and (ii) they do not scale with respect to the size of graphs in the database. We present GRAPES, software for parallel searching on databases of large biological graphs. GRAPES implements a parallel version

SUBMITTER: Giugno R 

PROVIDER: S-EPMC3805575 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature