title: Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment.
abstract: BACKGROUND
  Bioinformatics algorithms and computing power are the main bottlenecks for analyzing huge amount of data generated by the current technologies, such as the 'next-generation' sequencing methodologies. At the same time, most powerful microprocessors are based on many-core chips, yet most applications cannot exploit such power, requiring parallelized algorithms. As an example of next-generation bioinformatics, we have developed from scratch a new parallelization of the Needleman-Wunsch (NW) sequence alignment algorithm for the 64-core Tile64 microprocessor. The unprecedented performance it offers for a standalone personal computer (PC) is discussed, optimally aligning sequences up to 20 times faster than the non-parallelized version, thus saving valuable time.
  
  
  BACKGROUND
  This algorithm is available as a free web service for the scientific community at http://www.sicuma.uma.es/multicore. The open source code is also available on such site.
authors.affiliation: Department Lenguajes y Ciencias de la Computación, Universidad de Málaga 29071 Málaga, Spain. galvez@uma.es
authors.forename: Sergio
authors.initials: S
authors.lastname: Gálvez
authors.forename: David
authors.initials: D
authors.lastname: Díaz
authors.forename: Pilar
authors.initials: P
authors.lastname: Hernández
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Esteban
authors.forename: Juan A
authors.initials: JA
authors.lastname: Caballero
authors.forename: Gabriel
authors.initials: G
authors.lastname: Dorado
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D016415:Sequence Alignment / Q000379:methods*