title: A pluggable framework for parallel pairwise sequence search.
abstract: The current and near future of the computing industry is one of multi-core and multi-processor technology. Most existing sequence-search tools have been designed with a focus on single-core, single-processor systems. This discrepancy between software design and hardware architecture substantially hinders sequence-search performance by not allowing full utilization of the hardware. This paper presents a novel framework that will aid the conversion of serial sequence-search tools into a parallel version that can take full advantage of the available hardware. The framework, which is based on a software architecture called mixin layers with refined roles, enables modules to be plugged into the framework with minimal effort. The inherent modular design improves maintenance and extensibility, thus opening up a plethora of opportunities for advanced algorithmic features to be developed and incorporated while routine maintenance of the codebase persists.
authors.affiliation: Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA. jsarch@cs.vt.edu
authors.forename: Jeremy
authors.initials: J
authors.lastname: Archuleta
authors.forename: Wu-chun
authors.initials: WC
authors.lastname: Feng
authors.forename: Eli
authors.initials: E
authors.lastname: Tilevich
mesh_terms: D000465:Algorithms; D003199:Computer Systems; D016247:Information Storage and Retrieval / Q000379:methods*; D012984:Software